https://wiki.geneontology.org/api.php?action=feedcontributions&user=Hla28&feedformat=atomGO Wiki - User contributions [en]2024-03-28T21:21:54ZUser contributionsMediaWiki 1.40.0https://wiki.geneontology.org/index.php?title=LncRNA_GO_annotation_manual&diff=86724LncRNA GO annotation manual2024-03-15T12:35:51Z<p>Hla28: /* Random inactivation of X chromosome */</p>
<hr />
<div>LncRNAs have multiple and varied activities (see [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]] which describes 13 roles of lncRNAs), these guidelines are suggestions for the curation of some of these lncRNAs. These were discussed [https://github.com/geneontology/go-ontology/issues/23028 here].<br />
<br />
===Decision tree to assist with curation of lncRNA:miRNA interactions===<br />
<br />
These guidelines are for the curation of lncRNAs that bind to miRNA and prevent miRNA activity. These lncRNAs are may be described as miRNA sponges, decoys or competing endogenous RNAs. In these instances, the lncRNA may be destroyed as part of the process. As such, there needs to be a large excess of lncRNA over the miRNA target to be effective. Target-directed microRNA degradation is a distinct process where the lncRNA is not consummed and so the lncRNA does not need to be in massive excess over the miRNA target.<br />
<br />
Link to LncRNA_Decision_Tree pdf[[https://wiki.geneontology.org/images/e/e4/LncRNA_Decision_Tree.pdf]]<br />
<br />
[[File:LncRNA Decision Tree.jpg|960x540px]]<br />
<br />
'''Decision Tree for the GO terms and annotation extensions used for capturing targets of lncRNAs.''' The types of evidence in the blue boxes are described further in the text. Information about the cell or tissue that the interaction occurs in can be captured for example in the annotation extension field using: occurs_in (insert cell ontology ID and/or UBERON ID based on cell and/or tissue type respectively). This information can be included when inhibition of the lncRNA leads to an increase in the endogenous miRNA (or decrease in the miRNA target protein level). Slightly weaker evidence to support inclusion of the cell or tissue information would be evidence that the lncRNA is expressed in these cells/this tissue AND that the authors are confident that the lncRNA target is also being regulated in these cells/this tissue. For example, when the addition of the lncRNA leads to a decrease in the endogenous miRNA or increase in the endogenous protein level.<br />
<br />
'''Note:''' to be able to indicate any target in a GO annotation, the prediction evidence does not need to be in the paper you are annotating, it could be from another paper or a prediction database. When looking at predictions or validations in a prediction database, it is recommended to check the references cited for the target as they may serve as a good source of experimental annotation. Additionally, it has been found that some of the cited papers do not support the validation of the targets. Annotations to “miRNA inhibitor activity via base pairing” (GO:0140869) should ONLY be made from the paper containing the experimental evidence, however it is acceptable to indicate in the annotation extension of a “gene silencing by miRNA” annotation that the target of gene silencing is direct (by using ''has_input'') if the evidence for binding is in another paper.<br />
<br />
===Random inactivation of X chromosome===<br />
<br />
Figure 2b [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: Xist modulates inactive X chromosome (Xi) architecture during X chromosome inactivation (XCI).<br />
<br />
Annotation Example: The Xist lncRNA interacts directly with SHARP to silence transcription through HDAC3. [[https://pubmed.ncbi.nlm.nih.gov/31048766/25915022 PMID:25915022]]. <br />
<br />
LncRNA (mouse Xist URS000077A8CE_10090) Annotations:<br />
* MF: GO:0140463 chromatin-protein adaptor activity<br />
* BF: GO:0060816 random inactivation of X chromosome<br />
<br />
=== Intrachromosomal interactions via DNA-protein interactions ===<br />
<br />
Figure 2c [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: Firre transcripts localize to their transcription site and five additional autosomal chromosomal loci in trans to affect interactions between distant genomic regions.<br />
<br />
LncRNA (Firre) annotations:<br />
* MF: GO:0106260 DNA-DNA tethering activity + appropriate information etc (eg part_of GO:0006325 chromatin organization)<br />
* BP: GO:0006325 chromatin organization<br />
<br />
=== Promoter-enhancer loop anchoring activity ===<br />
<br />
Figure 2d [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: CCAT1-L accumulates in cis to modulate chromatin loops between enhancers and the promoter of MYC.<br />
<br />
LncRNA (CCAT1-L) annotations:<br />
* MF: GO:0140585 promoter-enhancer loop anchoring activity + appropriate information etc (eg part_of GO:0140588 chromatin looping)<br />
* BP: GO:0140588 chromatin looping<br />
<br />
=== Regulation of chromatin accessibility ===<br />
<br />
Figure 2e [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: lncRNAs regulate chromatin accessibility. Left, Xist recruits HDAC1-associated repressor protein (SHARP), silencing the mediator for retinoid and thyroid hormone receptor (SMART) and HDAC3 to silence Xi. Right, Mhrt prevents SWI/SNF binding to corresponding DNA loci.<br />
<br />
LncRNA (Xist) annotations:<br />
* MF: GO:0030674 protein-macromolecule adaptor activity + appropriate information (eg part_of GO:0006338 chromatin remodeling)<br />
* BP: GO:0006338 chromatin remodeling<br />
<br />
LncRNA (Mhrt) annotations based on [[https://pubmed.ncbi.nlm.nih.gov/25119045/ PMID:25119045]]:<br />
* MF: GO:0140311 protein sequestering activity + appropriate information etc (eg has_inputs Brg1/Smarca4, Q3TKT4), part_of GO:0006338 chromatin remodeling)<br />
* BP: GO:0006338 chromatin remodeling<br />
<br />
=== Triplex-Mediated Changes in Chromatin Structure ===<br />
<br />
Figure 2f, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: Khps1 enhances Pol II transcription by forming an R-loop that anchors Khps1-interacting p300/CBP to the SPHK1 promoter.<br />
<br />
LncRNA (Khps1) annotations based on [[https://pubmed.ncbi.nlm.nih.gov/26590717/ PMID: 26590717]]:<br />
<br />
* MF: GO:0030674 protein-macromolecule adaptor activity or GO:0001010 RNA polymerase II sequence-specific DNA-binding transcription factor recruiting activity + appropriate information etc (eg part_of GO:0045944 positive regulation of transcription by RNA polymerase II)<br />
* MF: GO:1990837 sequence-specific double-stranded DNA binding + appropriate information etc (eg part_of GO:0006325 chromatin organization)<br />
* BP: GO:0006325 chromatin organization<br />
* BP: GO:0045944 positive regulation of transcription by RNA polymerase II<br />
<br />
=== RNA polymerase inhibitor activity ===<br />
<br />
Figure 2g, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]:lncRNAs interfere with Pol II transcription machineries both at the initiation (left) and elongation (right) stages.<br />
<br />
LncRNA annotations:<br />
* MF: GO:0140870 RNA polymerase inhibitor activity<br />
* BP:GO:0000122 negative regulation of transcription by RNA polymerase II<br />
<br />
=== repressor of RNA polymerase inhibitor activity ===<br />
<br />
Figure 2h, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: SLERT promotes Pol I transcription by binding DDX21 to alter its conformation, thereby releasing its inhibitory effect on Pol I.<br />
<br />
LncRNA (SLERT) annotations:<br />
* MF: GO:0140871 repressor of RNA polymerase inhibitor activity + appropriate information (eg has_input DDX21)<br />
* BP: GO:0045943 positive regulation of transcription by RNA polymerase I<br />
<br />
=== molecular condensate scaffold activity ===<br />
<br />
Figure 2i, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: NEAT1 is an architectural lncRNA that nucleates paraspeckles. Upon cellular stress, altered NEAT1 transcription and processing lead to changes of paraspeckles. PSP, paraspeckle proteins.<br />
<br />
LncRNA (NEAT1) annotations:<br />
* MF: GO:0140693 molecular condensate scaffold activity + additional information (eg part_of GO:0006325 chromatin organization or GO:0006996 organelle organization)<br />
* BP: GO:0030575 nuclear body organization<br />
<br />
=== miRNA inhibitor activity ===<br />
<br />
See decision tree above <br />
Figure 2k, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]:Cyrano, harbouring miR-7 binding site and mediates its destruction by target-RNA-directed miRNA degradation.<br />
<br />
<br />
LncRNA Cyrano annotations e.g. mouse, URS000075A502_10090, URS000075B8A8_10090 [[https://pubmed.ncbi.nlm.nih.gov/29887379/ PMID:29887379]]. A Network of Noncoding Regulatory RNAs Acts in the Mammalian Brain. (2018)<br />
* MF GO:0140869 miRNA inhibitor activity via base-pairing<br />
** has_input URS0000591950_10090 (miR-7b-5p)& URS000075DE8D_10090 (miR-7a-5p) <br />
* BP: GO:0000512 lncRNA-mediated post-transcriptional gene silencing<br />
* BP: GO:0140958 target-directed miRNA degradation<br />
<br />
Note that the level of Cyrano does not change but the level of target miR-7 is down-regulated dramatically, as the lncRNA is not destroyed in the process. If the lncRNA decreases with the miRNA, then it is not target-directed miRNA degradation, but can be annotated with another more appropriate term such as GO:0010587 miRNA catabolic process.<br />
<br />
=== mRNA degradation ===<br />
<br />
Figure 2l, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: lncRNAs modulate mRNA stability by associating with proteins involved in mRNA degradation. Left, double-stranded RNAs formed by Alu-containing lncRNAs with mRNA 3′ UTRs recruit STAU1 to induce STAU1-mediated mRNA decay (SMD). Right, NORAD stabilizes PUMILIO 1/2 (PUM1/2)-targeted mRNAs via sequestering PUM1/2 from mRNAs.<br />
<br />
LncRNA (NORAD) annotations:<br />
* MF: GO:1903231 mRNA base-pairing translational repressor activity + additional information (eg part_of GO:0000512 lncRNA-mediated post-transcriptional gene silencing)<br />
* BP: GO:0000512 lncRNA-mediated post-transcriptional gene silencing<br />
<br />
=== mRNA translation repression ===<br />
<br />
Figure 2m, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: lncRNAs regulate translation. Association of lincRNA-p21 (linc-p21) with HuR favours the recruitment of let-7/Ago2, leading to its destabilization. In the absence of HuR, lincRNA-p21 identifies mRNA targets to repress their translation by recruiting the translation repressor Rck129. RISC, RNA-induced silencing complex.<br />
<br />
LncRNA annotations:<br />
* MF: GO:1903231 mRNA base-pairing translational repressor activity + additional information (eg part_of GO:0000512 lncRNA-mediated post-transcriptional gene silencing)<br />
* BP: GO:0000512 lncRNA-mediated post-transcriptional gene silencing<br />
<br />
=== regulation of post-translational modifications ===<br />
<br />
Figure 2n, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: lncRNAs modulate post-translational modifications. Lnc-DC directly interacts with STAT3 to prevent its dephosphorylation by SHP1 (PTPN6).<br />
<br />
<br />
LncRNA annotations URS00007B42BD_9606 (GenBank:KJ020271) and URS00007B3652_9606 (GenBank:KJ020272) from [[https://pubmed.ncbi.nlm.nih.gov/24744378/ PMID:24744378]] 'The STAT3-binding long noncoding RNA lnc-DC controls human dendritic cell differentiation'.<br />
* MF: GO:0019212 phosphatase inhibitor activity<br />
**has_input UniProtKB:P29350 (PTPN6)<br />
* MF: GO:0097677 STAT family protein binding<br />
**has_input UniProtKB:P40763 (STAT3)<br />
<br />
BP terms to describe regulation of pathway and involvement in processes:<br />
* BP: GO:0046427 positive regulation of receptor signaling pathway via JAK-STAT<br />
* BP: GO0097028 dendritic cell differentiation<br />
<br />
<br />
[[Category:Annotation Guidelines]]</div>Hla28https://wiki.geneontology.org/index.php?title=LncRNA_GO_annotation_manual&diff=86723LncRNA GO annotation manual2024-03-15T12:35:19Z<p>Hla28: /* Random inactivation of X chromosome */</p>
<hr />
<div>LncRNAs have multiple and varied activities (see [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]] which describes 13 roles of lncRNAs), these guidelines are suggestions for the curation of some of these lncRNAs. These were discussed [https://github.com/geneontology/go-ontology/issues/23028 here].<br />
<br />
===Decision tree to assist with curation of lncRNA:miRNA interactions===<br />
<br />
These guidelines are for the curation of lncRNAs that bind to miRNA and prevent miRNA activity. These lncRNAs are may be described as miRNA sponges, decoys or competing endogenous RNAs. In these instances, the lncRNA may be destroyed as part of the process. As such, there needs to be a large excess of lncRNA over the miRNA target to be effective. Target-directed microRNA degradation is a distinct process where the lncRNA is not consummed and so the lncRNA does not need to be in massive excess over the miRNA target.<br />
<br />
Link to LncRNA_Decision_Tree pdf[[https://wiki.geneontology.org/images/e/e4/LncRNA_Decision_Tree.pdf]]<br />
<br />
[[File:LncRNA Decision Tree.jpg|960x540px]]<br />
<br />
'''Decision Tree for the GO terms and annotation extensions used for capturing targets of lncRNAs.''' The types of evidence in the blue boxes are described further in the text. Information about the cell or tissue that the interaction occurs in can be captured for example in the annotation extension field using: occurs_in (insert cell ontology ID and/or UBERON ID based on cell and/or tissue type respectively). This information can be included when inhibition of the lncRNA leads to an increase in the endogenous miRNA (or decrease in the miRNA target protein level). Slightly weaker evidence to support inclusion of the cell or tissue information would be evidence that the lncRNA is expressed in these cells/this tissue AND that the authors are confident that the lncRNA target is also being regulated in these cells/this tissue. For example, when the addition of the lncRNA leads to a decrease in the endogenous miRNA or increase in the endogenous protein level.<br />
<br />
'''Note:''' to be able to indicate any target in a GO annotation, the prediction evidence does not need to be in the paper you are annotating, it could be from another paper or a prediction database. When looking at predictions or validations in a prediction database, it is recommended to check the references cited for the target as they may serve as a good source of experimental annotation. Additionally, it has been found that some of the cited papers do not support the validation of the targets. Annotations to “miRNA inhibitor activity via base pairing” (GO:0140869) should ONLY be made from the paper containing the experimental evidence, however it is acceptable to indicate in the annotation extension of a “gene silencing by miRNA” annotation that the target of gene silencing is direct (by using ''has_input'') if the evidence for binding is in another paper.<br />
<br />
===Random inactivation of X chromosome===<br />
<br />
Figure 2b [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: Xist modulates inactive X chromosome (Xi) architecture during X chromosome inactivation (XCI).<br />
<br />
Annotation Example: The Xist lncRNA interacts directly with SHARP to silence transcription through HDAC3. [[https://pubmed.ncbi.nlm.nih.gov/31048766/25915022 PMID:25915022]]. <br />
LncRNA (mouse Xist URS000077A8CE_10090) Annotations:<br />
* MF: GO:0140463 chromatin-protein adaptor activity<br />
* BF: GO:0060816 random inactivation of X chromosome<br />
<br />
=== Intrachromosomal interactions via DNA-protein interactions ===<br />
<br />
Figure 2c [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: Firre transcripts localize to their transcription site and five additional autosomal chromosomal loci in trans to affect interactions between distant genomic regions.<br />
<br />
LncRNA (Firre) annotations:<br />
* MF: GO:0106260 DNA-DNA tethering activity + appropriate information etc (eg part_of GO:0006325 chromatin organization)<br />
* BP: GO:0006325 chromatin organization<br />
<br />
=== Promoter-enhancer loop anchoring activity ===<br />
<br />
Figure 2d [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: CCAT1-L accumulates in cis to modulate chromatin loops between enhancers and the promoter of MYC.<br />
<br />
LncRNA (CCAT1-L) annotations:<br />
* MF: GO:0140585 promoter-enhancer loop anchoring activity + appropriate information etc (eg part_of GO:0140588 chromatin looping)<br />
* BP: GO:0140588 chromatin looping<br />
<br />
=== Regulation of chromatin accessibility ===<br />
<br />
Figure 2e [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: lncRNAs regulate chromatin accessibility. Left, Xist recruits HDAC1-associated repressor protein (SHARP), silencing the mediator for retinoid and thyroid hormone receptor (SMART) and HDAC3 to silence Xi. Right, Mhrt prevents SWI/SNF binding to corresponding DNA loci.<br />
<br />
LncRNA (Xist) annotations:<br />
* MF: GO:0030674 protein-macromolecule adaptor activity + appropriate information (eg part_of GO:0006338 chromatin remodeling)<br />
* BP: GO:0006338 chromatin remodeling<br />
<br />
LncRNA (Mhrt) annotations based on [[https://pubmed.ncbi.nlm.nih.gov/25119045/ PMID:25119045]]:<br />
* MF: GO:0140311 protein sequestering activity + appropriate information etc (eg has_inputs Brg1/Smarca4, Q3TKT4), part_of GO:0006338 chromatin remodeling)<br />
* BP: GO:0006338 chromatin remodeling<br />
<br />
=== Triplex-Mediated Changes in Chromatin Structure ===<br />
<br />
Figure 2f, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: Khps1 enhances Pol II transcription by forming an R-loop that anchors Khps1-interacting p300/CBP to the SPHK1 promoter.<br />
<br />
LncRNA (Khps1) annotations based on [[https://pubmed.ncbi.nlm.nih.gov/26590717/ PMID: 26590717]]:<br />
<br />
* MF: GO:0030674 protein-macromolecule adaptor activity or GO:0001010 RNA polymerase II sequence-specific DNA-binding transcription factor recruiting activity + appropriate information etc (eg part_of GO:0045944 positive regulation of transcription by RNA polymerase II)<br />
* MF: GO:1990837 sequence-specific double-stranded DNA binding + appropriate information etc (eg part_of GO:0006325 chromatin organization)<br />
* BP: GO:0006325 chromatin organization<br />
* BP: GO:0045944 positive regulation of transcription by RNA polymerase II<br />
<br />
=== RNA polymerase inhibitor activity ===<br />
<br />
Figure 2g, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]:lncRNAs interfere with Pol II transcription machineries both at the initiation (left) and elongation (right) stages.<br />
<br />
LncRNA annotations:<br />
* MF: GO:0140870 RNA polymerase inhibitor activity<br />
* BP:GO:0000122 negative regulation of transcription by RNA polymerase II<br />
<br />
=== repressor of RNA polymerase inhibitor activity ===<br />
<br />
Figure 2h, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: SLERT promotes Pol I transcription by binding DDX21 to alter its conformation, thereby releasing its inhibitory effect on Pol I.<br />
<br />
LncRNA (SLERT) annotations:<br />
* MF: GO:0140871 repressor of RNA polymerase inhibitor activity + appropriate information (eg has_input DDX21)<br />
* BP: GO:0045943 positive regulation of transcription by RNA polymerase I<br />
<br />
=== molecular condensate scaffold activity ===<br />
<br />
Figure 2i, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: NEAT1 is an architectural lncRNA that nucleates paraspeckles. Upon cellular stress, altered NEAT1 transcription and processing lead to changes of paraspeckles. PSP, paraspeckle proteins.<br />
<br />
LncRNA (NEAT1) annotations:<br />
* MF: GO:0140693 molecular condensate scaffold activity + additional information (eg part_of GO:0006325 chromatin organization or GO:0006996 organelle organization)<br />
* BP: GO:0030575 nuclear body organization<br />
<br />
=== miRNA inhibitor activity ===<br />
<br />
See decision tree above <br />
Figure 2k, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]:Cyrano, harbouring miR-7 binding site and mediates its destruction by target-RNA-directed miRNA degradation.<br />
<br />
<br />
LncRNA Cyrano annotations e.g. mouse, URS000075A502_10090, URS000075B8A8_10090 [[https://pubmed.ncbi.nlm.nih.gov/29887379/ PMID:29887379]]. A Network of Noncoding Regulatory RNAs Acts in the Mammalian Brain. (2018)<br />
* MF GO:0140869 miRNA inhibitor activity via base-pairing<br />
** has_input URS0000591950_10090 (miR-7b-5p)& URS000075DE8D_10090 (miR-7a-5p) <br />
* BP: GO:0000512 lncRNA-mediated post-transcriptional gene silencing<br />
* BP: GO:0140958 target-directed miRNA degradation<br />
<br />
Note that the level of Cyrano does not change but the level of target miR-7 is down-regulated dramatically, as the lncRNA is not destroyed in the process. If the lncRNA decreases with the miRNA, then it is not target-directed miRNA degradation, but can be annotated with another more appropriate term such as GO:0010587 miRNA catabolic process.<br />
<br />
=== mRNA degradation ===<br />
<br />
Figure 2l, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: lncRNAs modulate mRNA stability by associating with proteins involved in mRNA degradation. Left, double-stranded RNAs formed by Alu-containing lncRNAs with mRNA 3′ UTRs recruit STAU1 to induce STAU1-mediated mRNA decay (SMD). Right, NORAD stabilizes PUMILIO 1/2 (PUM1/2)-targeted mRNAs via sequestering PUM1/2 from mRNAs.<br />
<br />
LncRNA (NORAD) annotations:<br />
* MF: GO:1903231 mRNA base-pairing translational repressor activity + additional information (eg part_of GO:0000512 lncRNA-mediated post-transcriptional gene silencing)<br />
* BP: GO:0000512 lncRNA-mediated post-transcriptional gene silencing<br />
<br />
=== mRNA translation repression ===<br />
<br />
Figure 2m, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: lncRNAs regulate translation. Association of lincRNA-p21 (linc-p21) with HuR favours the recruitment of let-7/Ago2, leading to its destabilization. In the absence of HuR, lincRNA-p21 identifies mRNA targets to repress their translation by recruiting the translation repressor Rck129. RISC, RNA-induced silencing complex.<br />
<br />
LncRNA annotations:<br />
* MF: GO:1903231 mRNA base-pairing translational repressor activity + additional information (eg part_of GO:0000512 lncRNA-mediated post-transcriptional gene silencing)<br />
* BP: GO:0000512 lncRNA-mediated post-transcriptional gene silencing<br />
<br />
=== regulation of post-translational modifications ===<br />
<br />
Figure 2n, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: lncRNAs modulate post-translational modifications. Lnc-DC directly interacts with STAT3 to prevent its dephosphorylation by SHP1 (PTPN6).<br />
<br />
<br />
LncRNA annotations URS00007B42BD_9606 (GenBank:KJ020271) and URS00007B3652_9606 (GenBank:KJ020272) from [[https://pubmed.ncbi.nlm.nih.gov/24744378/ PMID:24744378]] 'The STAT3-binding long noncoding RNA lnc-DC controls human dendritic cell differentiation'.<br />
* MF: GO:0019212 phosphatase inhibitor activity<br />
**has_input UniProtKB:P29350 (PTPN6)<br />
* MF: GO:0097677 STAT family protein binding<br />
**has_input UniProtKB:P40763 (STAT3)<br />
<br />
BP terms to describe regulation of pathway and involvement in processes:<br />
* BP: GO:0046427 positive regulation of receptor signaling pathway via JAK-STAT<br />
* BP: GO0097028 dendritic cell differentiation<br />
<br />
<br />
[[Category:Annotation Guidelines]]</div>Hla28https://wiki.geneontology.org/index.php?title=LncRNA_GO_annotation_manual&diff=86722LncRNA GO annotation manual2024-03-15T12:33:46Z<p>Hla28: /* DNA-DNA tethering activity */</p>
<hr />
<div>LncRNAs have multiple and varied activities (see [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]] which describes 13 roles of lncRNAs), these guidelines are suggestions for the curation of some of these lncRNAs. These were discussed [https://github.com/geneontology/go-ontology/issues/23028 here].<br />
<br />
===Decision tree to assist with curation of lncRNA:miRNA interactions===<br />
<br />
These guidelines are for the curation of lncRNAs that bind to miRNA and prevent miRNA activity. These lncRNAs are may be described as miRNA sponges, decoys or competing endogenous RNAs. In these instances, the lncRNA may be destroyed as part of the process. As such, there needs to be a large excess of lncRNA over the miRNA target to be effective. Target-directed microRNA degradation is a distinct process where the lncRNA is not consummed and so the lncRNA does not need to be in massive excess over the miRNA target.<br />
<br />
Link to LncRNA_Decision_Tree pdf[[https://wiki.geneontology.org/images/e/e4/LncRNA_Decision_Tree.pdf]]<br />
<br />
[[File:LncRNA Decision Tree.jpg|960x540px]]<br />
<br />
'''Decision Tree for the GO terms and annotation extensions used for capturing targets of lncRNAs.''' The types of evidence in the blue boxes are described further in the text. Information about the cell or tissue that the interaction occurs in can be captured for example in the annotation extension field using: occurs_in (insert cell ontology ID and/or UBERON ID based on cell and/or tissue type respectively). This information can be included when inhibition of the lncRNA leads to an increase in the endogenous miRNA (or decrease in the miRNA target protein level). Slightly weaker evidence to support inclusion of the cell or tissue information would be evidence that the lncRNA is expressed in these cells/this tissue AND that the authors are confident that the lncRNA target is also being regulated in these cells/this tissue. For example, when the addition of the lncRNA leads to a decrease in the endogenous miRNA or increase in the endogenous protein level.<br />
<br />
'''Note:''' to be able to indicate any target in a GO annotation, the prediction evidence does not need to be in the paper you are annotating, it could be from another paper or a prediction database. When looking at predictions or validations in a prediction database, it is recommended to check the references cited for the target as they may serve as a good source of experimental annotation. Additionally, it has been found that some of the cited papers do not support the validation of the targets. Annotations to “miRNA inhibitor activity via base pairing” (GO:0140869) should ONLY be made from the paper containing the experimental evidence, however it is acceptable to indicate in the annotation extension of a “gene silencing by miRNA” annotation that the target of gene silencing is direct (by using ''has_input'') if the evidence for binding is in another paper.<br />
<br />
===Random inactivation of X chromosome===<br />
<br />
Figure 2b [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: Xist modulates inactive X chromosome (Xi) architecture during X chromosome inactivation (XCI) by recruiting Xi to associate with the lamin B receptor (LBR) at the nuclear lamina to silence transcription.<br />
<br />
The Xist lncRNA interacts directly with SHARP to silence transcription through HDAC3. [[https://pubmed.ncbi.nlm.nih.gov/31048766/25915022 PMID:25915022]]. <br />
<br />
LncRNA (mouse Xist URS000077A8CE_10090) Annotations:<br />
* MF: GO:0140463 chromatin-protein adaptor activity<br />
* BF: GO:0060816 random inactivation of X chromosome<br />
<br />
=== Intrachromosomal interactions via DNA-protein interactions ===<br />
<br />
Figure 2c [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: Firre transcripts localize to their transcription site and five additional autosomal chromosomal loci in trans to affect interactions between distant genomic regions.<br />
<br />
LncRNA (Firre) annotations:<br />
* MF: GO:0106260 DNA-DNA tethering activity + appropriate information etc (eg part_of GO:0006325 chromatin organization)<br />
* BP: GO:0006325 chromatin organization<br />
<br />
=== Promoter-enhancer loop anchoring activity ===<br />
<br />
Figure 2d [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: CCAT1-L accumulates in cis to modulate chromatin loops between enhancers and the promoter of MYC.<br />
<br />
LncRNA (CCAT1-L) annotations:<br />
* MF: GO:0140585 promoter-enhancer loop anchoring activity + appropriate information etc (eg part_of GO:0140588 chromatin looping)<br />
* BP: GO:0140588 chromatin looping<br />
<br />
=== Regulation of chromatin accessibility ===<br />
<br />
Figure 2e [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: lncRNAs regulate chromatin accessibility. Left, Xist recruits HDAC1-associated repressor protein (SHARP), silencing the mediator for retinoid and thyroid hormone receptor (SMART) and HDAC3 to silence Xi. Right, Mhrt prevents SWI/SNF binding to corresponding DNA loci.<br />
<br />
LncRNA (Xist) annotations:<br />
* MF: GO:0030674 protein-macromolecule adaptor activity + appropriate information (eg part_of GO:0006338 chromatin remodeling)<br />
* BP: GO:0006338 chromatin remodeling<br />
<br />
LncRNA (Mhrt) annotations based on [[https://pubmed.ncbi.nlm.nih.gov/25119045/ PMID:25119045]]:<br />
* MF: GO:0140311 protein sequestering activity + appropriate information etc (eg has_inputs Brg1/Smarca4, Q3TKT4), part_of GO:0006338 chromatin remodeling)<br />
* BP: GO:0006338 chromatin remodeling<br />
<br />
=== Triplex-Mediated Changes in Chromatin Structure ===<br />
<br />
Figure 2f, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: Khps1 enhances Pol II transcription by forming an R-loop that anchors Khps1-interacting p300/CBP to the SPHK1 promoter.<br />
<br />
LncRNA (Khps1) annotations based on [[https://pubmed.ncbi.nlm.nih.gov/26590717/ PMID: 26590717]]:<br />
<br />
* MF: GO:0030674 protein-macromolecule adaptor activity or GO:0001010 RNA polymerase II sequence-specific DNA-binding transcription factor recruiting activity + appropriate information etc (eg part_of GO:0045944 positive regulation of transcription by RNA polymerase II)<br />
* MF: GO:1990837 sequence-specific double-stranded DNA binding + appropriate information etc (eg part_of GO:0006325 chromatin organization)<br />
* BP: GO:0006325 chromatin organization<br />
* BP: GO:0045944 positive regulation of transcription by RNA polymerase II<br />
<br />
=== RNA polymerase inhibitor activity ===<br />
<br />
Figure 2g, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]:lncRNAs interfere with Pol II transcription machineries both at the initiation (left) and elongation (right) stages.<br />
<br />
LncRNA annotations:<br />
* MF: GO:0140870 RNA polymerase inhibitor activity<br />
* BP:GO:0000122 negative regulation of transcription by RNA polymerase II<br />
<br />
=== repressor of RNA polymerase inhibitor activity ===<br />
<br />
Figure 2h, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: SLERT promotes Pol I transcription by binding DDX21 to alter its conformation, thereby releasing its inhibitory effect on Pol I.<br />
<br />
LncRNA (SLERT) annotations:<br />
* MF: GO:0140871 repressor of RNA polymerase inhibitor activity + appropriate information (eg has_input DDX21)<br />
* BP: GO:0045943 positive regulation of transcription by RNA polymerase I<br />
<br />
=== molecular condensate scaffold activity ===<br />
<br />
Figure 2i, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: NEAT1 is an architectural lncRNA that nucleates paraspeckles. Upon cellular stress, altered NEAT1 transcription and processing lead to changes of paraspeckles. PSP, paraspeckle proteins.<br />
<br />
LncRNA (NEAT1) annotations:<br />
* MF: GO:0140693 molecular condensate scaffold activity + additional information (eg part_of GO:0006325 chromatin organization or GO:0006996 organelle organization)<br />
* BP: GO:0030575 nuclear body organization<br />
<br />
=== miRNA inhibitor activity ===<br />
<br />
See decision tree above <br />
Figure 2k, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]:Cyrano, harbouring miR-7 binding site and mediates its destruction by target-RNA-directed miRNA degradation.<br />
<br />
<br />
LncRNA Cyrano annotations e.g. mouse, URS000075A502_10090, URS000075B8A8_10090 [[https://pubmed.ncbi.nlm.nih.gov/29887379/ PMID:29887379]]. A Network of Noncoding Regulatory RNAs Acts in the Mammalian Brain. (2018)<br />
* MF GO:0140869 miRNA inhibitor activity via base-pairing<br />
** has_input URS0000591950_10090 (miR-7b-5p)& URS000075DE8D_10090 (miR-7a-5p) <br />
* BP: GO:0000512 lncRNA-mediated post-transcriptional gene silencing<br />
* BP: GO:0140958 target-directed miRNA degradation<br />
<br />
Note that the level of Cyrano does not change but the level of target miR-7 is down-regulated dramatically, as the lncRNA is not destroyed in the process. If the lncRNA decreases with the miRNA, then it is not target-directed miRNA degradation, but can be annotated with another more appropriate term such as GO:0010587 miRNA catabolic process.<br />
<br />
=== mRNA degradation ===<br />
<br />
Figure 2l, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: lncRNAs modulate mRNA stability by associating with proteins involved in mRNA degradation. Left, double-stranded RNAs formed by Alu-containing lncRNAs with mRNA 3′ UTRs recruit STAU1 to induce STAU1-mediated mRNA decay (SMD). Right, NORAD stabilizes PUMILIO 1/2 (PUM1/2)-targeted mRNAs via sequestering PUM1/2 from mRNAs.<br />
<br />
LncRNA (NORAD) annotations:<br />
* MF: GO:1903231 mRNA base-pairing translational repressor activity + additional information (eg part_of GO:0000512 lncRNA-mediated post-transcriptional gene silencing)<br />
* BP: GO:0000512 lncRNA-mediated post-transcriptional gene silencing<br />
<br />
=== mRNA translation repression ===<br />
<br />
Figure 2m, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: lncRNAs regulate translation. Association of lincRNA-p21 (linc-p21) with HuR favours the recruitment of let-7/Ago2, leading to its destabilization. In the absence of HuR, lincRNA-p21 identifies mRNA targets to repress their translation by recruiting the translation repressor Rck129. RISC, RNA-induced silencing complex.<br />
<br />
LncRNA annotations:<br />
* MF: GO:1903231 mRNA base-pairing translational repressor activity + additional information (eg part_of GO:0000512 lncRNA-mediated post-transcriptional gene silencing)<br />
* BP: GO:0000512 lncRNA-mediated post-transcriptional gene silencing<br />
<br />
=== regulation of post-translational modifications ===<br />
<br />
Figure 2n, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: lncRNAs modulate post-translational modifications. Lnc-DC directly interacts with STAT3 to prevent its dephosphorylation by SHP1 (PTPN6).<br />
<br />
<br />
LncRNA annotations URS00007B42BD_9606 (GenBank:KJ020271) and URS00007B3652_9606 (GenBank:KJ020272) from [[https://pubmed.ncbi.nlm.nih.gov/24744378/ PMID:24744378]] 'The STAT3-binding long noncoding RNA lnc-DC controls human dendritic cell differentiation'.<br />
* MF: GO:0019212 phosphatase inhibitor activity<br />
**has_input UniProtKB:P29350 (PTPN6)<br />
* MF: GO:0097677 STAT family protein binding<br />
**has_input UniProtKB:P40763 (STAT3)<br />
<br />
BP terms to describe regulation of pathway and involvement in processes:<br />
* BP: GO:0046427 positive regulation of receptor signaling pathway via JAK-STAT<br />
* BP: GO0097028 dendritic cell differentiation<br />
<br />
<br />
[[Category:Annotation Guidelines]]</div>Hla28https://wiki.geneontology.org/index.php?title=LncRNA_GO_annotation_manual&diff=86643LncRNA GO annotation manual2024-03-06T23:07:47Z<p>Hla28: /* Random inactivation of X chromosome */</p>
<hr />
<div>LncRNAs have multiple and varied activities (see [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]] which describes 13 roles of lncRNAs), these guidelines are suggestions for the curation of some of these lncRNAs. These were discussed [https://github.com/geneontology/go-ontology/issues/23028 here].<br />
<br />
===Decision tree to assist with curation of lncRNA:miRNA interactions===<br />
<br />
These guidelines are for the curation of lncRNAs that bind to miRNA and prevent miRNA activity. These lncRNAs are may be described as miRNA sponges, decoys or competing endogenous RNAs. In these instances, the lncRNA may be destroyed as part of the process. As such, there needs to be a large excess of lncRNA over the miRNA target to be effective. Target-directed microRNA degradation is a distinct process where the lncRNA is not consummed and so the lncRNA does not need to be in massive excess over the miRNA target.<br />
<br />
Link to LncRNA_Decision_Tree pdf[[https://wiki.geneontology.org/images/e/e4/LncRNA_Decision_Tree.pdf]]<br />
<br />
[[File:LncRNA Decision Tree.jpg|960x540px]]<br />
<br />
'''Decision Tree for the GO terms and annotation extensions used for capturing targets of lncRNAs.''' The types of evidence in the blue boxes are described further in the text. Information about the cell or tissue that the interaction occurs in can be captured for example in the annotation extension field using: occurs_in (insert cell ontology ID and/or UBERON ID based on cell and/or tissue type respectively). This information can be included when inhibition of the lncRNA leads to an increase in the endogenous miRNA (or decrease in the miRNA target protein level). Slightly weaker evidence to support inclusion of the cell or tissue information would be evidence that the lncRNA is expressed in these cells/this tissue AND that the authors are confident that the lncRNA target is also being regulated in these cells/this tissue. For example, when the addition of the lncRNA leads to a decrease in the endogenous miRNA or increase in the endogenous protein level.<br />
<br />
'''Note:''' to be able to indicate any target in a GO annotation, the prediction evidence does not need to be in the paper you are annotating, it could be from another paper or a prediction database. When looking at predictions or validations in a prediction database, it is recommended to check the references cited for the target as they may serve as a good source of experimental annotation. Additionally, it has been found that some of the cited papers do not support the validation of the targets. Annotations to “miRNA inhibitor activity via base pairing” (GO:0140869) should ONLY be made from the paper containing the experimental evidence, however it is acceptable to indicate in the annotation extension of a “gene silencing by miRNA” annotation that the target of gene silencing is direct (by using ''has_input'') if the evidence for binding is in another paper.<br />
<br />
===Random inactivation of X chromosome===<br />
<br />
Figure 2b [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: Xist modulates inactive X chromosome (Xi) architecture during X chromosome inactivation (XCI) by recruiting Xi to associate with the lamin B receptor (LBR) at the nuclear lamina to silence transcription.<br />
<br />
The Xist lncRNA interacts directly with SHARP to silence transcription through HDAC3. [[https://pubmed.ncbi.nlm.nih.gov/31048766/25915022 PMID:25915022]]. <br />
<br />
LncRNA (mouse Xist URS000077A8CE_10090) Annotations:<br />
* MF: GO:0140463 chromatin-protein adaptor activity<br />
* BF: GO:0060816 random inactivation of X chromosome<br />
<br />
=== DNA-DNA tethering activity ===<br />
<br />
Figure 2c [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: Firre transcripts localize to their transcription site and five additional autosomal chromosomal loci in trans to affect interactions between distant genomic regions.<br />
<br />
LncRNA (Firre) annotations:<br />
* MF: GO:0106260 DNA-DNA tethering activity + appropriate information etc (eg part_of GO:0006325 chromatin organization)<br />
* BP: GO:0006325 chromatin organization<br />
<br />
=== Promoter-enhancer loop anchoring activity ===<br />
<br />
Figure 2d [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: CCAT1-L accumulates in cis to modulate chromatin loops between enhancers and the promoter of MYC.<br />
<br />
LncRNA (CCAT1-L) annotations:<br />
* MF: GO:0140585 promoter-enhancer loop anchoring activity + appropriate information etc (eg part_of GO:0140588 chromatin looping)<br />
* BP: GO:0140588 chromatin looping<br />
<br />
=== Regulation of chromatin accessibility ===<br />
<br />
Figure 2e [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: lncRNAs regulate chromatin accessibility. Left, Xist recruits HDAC1-associated repressor protein (SHARP), silencing the mediator for retinoid and thyroid hormone receptor (SMART) and HDAC3 to silence Xi. Right, Mhrt prevents SWI/SNF binding to corresponding DNA loci.<br />
<br />
LncRNA (Xist) annotations:<br />
* MF: GO:0030674 protein-macromolecule adaptor activity + appropriate information (eg part_of GO:0006338 chromatin remodeling)<br />
* BP: GO:0006338 chromatin remodeling<br />
<br />
LncRNA (Mhrt) annotations based on [[https://pubmed.ncbi.nlm.nih.gov/25119045/ PMID:25119045]]:<br />
* MF: GO:0140311 protein sequestering activity + appropriate information etc (eg has_inputs Brg1/Smarca4, Q3TKT4), part_of GO:0006338 chromatin remodeling)<br />
* BP: GO:0006338 chromatin remodeling<br />
<br />
=== Triplex-Mediated Changes in Chromatin Structure ===<br />
<br />
Figure 2f, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: Khps1 enhances Pol II transcription by forming an R-loop that anchors Khps1-interacting p300/CBP to the SPHK1 promoter.<br />
<br />
LncRNA (Khps1) annotations based on [[https://pubmed.ncbi.nlm.nih.gov/26590717/ PMID: 26590717]]:<br />
<br />
* MF: GO:0030674 protein-macromolecule adaptor activity or GO:0001010 RNA polymerase II sequence-specific DNA-binding transcription factor recruiting activity + appropriate information etc (eg part_of GO:0045944 positive regulation of transcription by RNA polymerase II)<br />
* MF: GO:1990837 sequence-specific double-stranded DNA binding + appropriate information etc (eg part_of GO:0006325 chromatin organization)<br />
* BP: GO:0006325 chromatin organization<br />
* BP: GO:0045944 positive regulation of transcription by RNA polymerase II<br />
<br />
=== RNA polymerase inhibitor activity ===<br />
<br />
Figure 2g, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]:lncRNAs interfere with Pol II transcription machineries both at the initiation (left) and elongation (right) stages.<br />
<br />
LncRNA annotations:<br />
* MF: GO:0140870 RNA polymerase inhibitor activity<br />
* BP:GO:0000122 negative regulation of transcription by RNA polymerase II<br />
<br />
=== repressor of RNA polymerase inhibitor activity ===<br />
<br />
Figure 2h, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: SLERT promotes Pol I transcription by binding DDX21 to alter its conformation, thereby releasing its inhibitory effect on Pol I.<br />
<br />
LncRNA (SLERT) annotations:<br />
* MF: GO:0140871 repressor of RNA polymerase inhibitor activity + appropriate information (eg has_input DDX21)<br />
* BP: GO:0045943 positive regulation of transcription by RNA polymerase I<br />
<br />
=== molecular condensate scaffold activity ===<br />
<br />
Figure 2i, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: NEAT1 is an architectural lncRNA that nucleates paraspeckles. Upon cellular stress, altered NEAT1 transcription and processing lead to changes of paraspeckles. PSP, paraspeckle proteins.<br />
<br />
LncRNA (NEAT1) annotations:<br />
* MF: GO:0140693 molecular condensate scaffold activity + additional information (eg part_of GO:0006325 chromatin organization or GO:0006996 organelle organization)<br />
* BP: GO:0030575 nuclear body organization<br />
<br />
=== miRNA inhibitor activity ===<br />
<br />
See decision tree above <br />
Figure 2k, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]:Cyrano, harbouring miR-7 binding site and mediates its destruction by target-RNA-directed miRNA degradation.<br />
<br />
<br />
LncRNA Cyrano annotations e.g. mouse, URS000075A502_10090, URS000075B8A8_10090 [[https://pubmed.ncbi.nlm.nih.gov/29887379/ PMID:29887379]]. A Network of Noncoding Regulatory RNAs Acts in the Mammalian Brain. (2018)<br />
* MF GO:0140869 miRNA inhibitor activity via base-pairing<br />
** has_input URS0000591950_10090 (miR-7b-5p)& URS000075DE8D_10090 (miR-7a-5p) <br />
* BP: GO:0000512 lncRNA-mediated post-transcriptional gene silencing<br />
* BP: GO:0140958 target-directed miRNA degradation<br />
<br />
Note that the level of Cyrano does not change but the level of target miR-7 is down-regulated dramatically, as the lncRNA is not destroyed in the process. If the lncRNA decreases with the miRNA, then it is not target-directed miRNA degradation, but can be annotated with another more appropriate term such as GO:0010587 miRNA catabolic process.<br />
<br />
=== mRNA degradation ===<br />
<br />
Figure 2l, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: lncRNAs modulate mRNA stability by associating with proteins involved in mRNA degradation. Left, double-stranded RNAs formed by Alu-containing lncRNAs with mRNA 3′ UTRs recruit STAU1 to induce STAU1-mediated mRNA decay (SMD). Right, NORAD stabilizes PUMILIO 1/2 (PUM1/2)-targeted mRNAs via sequestering PUM1/2 from mRNAs.<br />
<br />
LncRNA (NORAD) annotations:<br />
* MF: GO:1903231 mRNA base-pairing translational repressor activity + additional information (eg part_of GO:0000512 lncRNA-mediated post-transcriptional gene silencing)<br />
* BP: GO:0000512 lncRNA-mediated post-transcriptional gene silencing<br />
<br />
=== mRNA translation repression ===<br />
<br />
Figure 2m, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: lncRNAs regulate translation. Association of lincRNA-p21 (linc-p21) with HuR favours the recruitment of let-7/Ago2, leading to its destabilization. In the absence of HuR, lincRNA-p21 identifies mRNA targets to repress their translation by recruiting the translation repressor Rck129. RISC, RNA-induced silencing complex.<br />
<br />
LncRNA annotations:<br />
* MF: GO:1903231 mRNA base-pairing translational repressor activity + additional information (eg part_of GO:0000512 lncRNA-mediated post-transcriptional gene silencing)<br />
* BP: GO:0000512 lncRNA-mediated post-transcriptional gene silencing<br />
<br />
=== regulation of post-translational modifications ===<br />
<br />
Figure 2n, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: lncRNAs modulate post-translational modifications. Lnc-DC directly interacts with STAT3 to prevent its dephosphorylation by SHP1 (PTPN6).<br />
<br />
<br />
LncRNA annotations URS00007B42BD_9606 (GenBank:KJ020271) and URS00007B3652_9606 (GenBank:KJ020272) from [[https://pubmed.ncbi.nlm.nih.gov/24744378/ PMID:24744378]] 'The STAT3-binding long noncoding RNA lnc-DC controls human dendritic cell differentiation'.<br />
* MF: GO:0019212 phosphatase inhibitor activity<br />
**has_input UniProtKB:P29350 (PTPN6)<br />
* MF: GO:0097677 STAT family protein binding<br />
**has_input UniProtKB:P40763 (STAT3)<br />
<br />
BP terms to describe regulation of pathway and involvement in processes:<br />
* BP: GO:0046427 positive regulation of receptor signaling pathway via JAK-STAT<br />
* BP: GO0097028 dendritic cell differentiation<br />
<br />
<br />
[[Category:Annotation Guidelines]]</div>Hla28https://wiki.geneontology.org/index.php?title=LncRNA_GO_annotation_manual&diff=86642LncRNA GO annotation manual2024-03-06T22:15:36Z<p>Hla28: /* Decision tree to assist with curation of lncRNA:miRNA interactions */</p>
<hr />
<div>LncRNAs have multiple and varied activities (see [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]] which describes 13 roles of lncRNAs), these guidelines are suggestions for the curation of some of these lncRNAs. These were discussed [https://github.com/geneontology/go-ontology/issues/23028 here].<br />
<br />
===Decision tree to assist with curation of lncRNA:miRNA interactions===<br />
<br />
These guidelines are for the curation of lncRNAs that bind to miRNA and prevent miRNA activity. These lncRNAs are may be described as miRNA sponges, decoys or competing endogenous RNAs. In these instances, the lncRNA may be destroyed as part of the process. As such, there needs to be a large excess of lncRNA over the miRNA target to be effective. Target-directed microRNA degradation is a distinct process where the lncRNA is not consummed and so the lncRNA does not need to be in massive excess over the miRNA target.<br />
<br />
Link to LncRNA_Decision_Tree pdf[[https://wiki.geneontology.org/images/e/e4/LncRNA_Decision_Tree.pdf]]<br />
<br />
[[File:LncRNA Decision Tree.jpg|960x540px]]<br />
<br />
'''Decision Tree for the GO terms and annotation extensions used for capturing targets of lncRNAs.''' The types of evidence in the blue boxes are described further in the text. Information about the cell or tissue that the interaction occurs in can be captured for example in the annotation extension field using: occurs_in (insert cell ontology ID and/or UBERON ID based on cell and/or tissue type respectively). This information can be included when inhibition of the lncRNA leads to an increase in the endogenous miRNA (or decrease in the miRNA target protein level). Slightly weaker evidence to support inclusion of the cell or tissue information would be evidence that the lncRNA is expressed in these cells/this tissue AND that the authors are confident that the lncRNA target is also being regulated in these cells/this tissue. For example, when the addition of the lncRNA leads to a decrease in the endogenous miRNA or increase in the endogenous protein level.<br />
<br />
'''Note:''' to be able to indicate any target in a GO annotation, the prediction evidence does not need to be in the paper you are annotating, it could be from another paper or a prediction database. When looking at predictions or validations in a prediction database, it is recommended to check the references cited for the target as they may serve as a good source of experimental annotation. Additionally, it has been found that some of the cited papers do not support the validation of the targets. Annotations to “miRNA inhibitor activity via base pairing” (GO:0140869) should ONLY be made from the paper containing the experimental evidence, however it is acceptable to indicate in the annotation extension of a “gene silencing by miRNA” annotation that the target of gene silencing is direct (by using ''has_input'') if the evidence for binding is in another paper.<br />
<br />
===Random inactivation of X chromosome===<br />
<br />
Figure 2b [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: Xist modulates inactive X chromosome (Xi) architecture during X chromosome inactivation (XCI) by recruiting Xi to associate with the lamin B receptor (LBR) at the nuclear lamina to silence transcription.<br />
<br />
LncRNA (Xist) Annotations:<br />
* MF: GO:0140463 chromatin-protein adaptor activity<br />
* BF: GO:0060816 random inactivation of X chromosome<br />
<br />
=== DNA-DNA tethering activity ===<br />
<br />
Figure 2c [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: Firre transcripts localize to their transcription site and five additional autosomal chromosomal loci in trans to affect interactions between distant genomic regions.<br />
<br />
LncRNA (Firre) annotations:<br />
* MF: GO:0106260 DNA-DNA tethering activity + appropriate information etc (eg part_of GO:0006325 chromatin organization)<br />
* BP: GO:0006325 chromatin organization<br />
<br />
=== Promoter-enhancer loop anchoring activity ===<br />
<br />
Figure 2d [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: CCAT1-L accumulates in cis to modulate chromatin loops between enhancers and the promoter of MYC.<br />
<br />
LncRNA (CCAT1-L) annotations:<br />
* MF: GO:0140585 promoter-enhancer loop anchoring activity + appropriate information etc (eg part_of GO:0140588 chromatin looping)<br />
* BP: GO:0140588 chromatin looping<br />
<br />
=== Regulation of chromatin accessibility ===<br />
<br />
Figure 2e [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: lncRNAs regulate chromatin accessibility. Left, Xist recruits HDAC1-associated repressor protein (SHARP), silencing the mediator for retinoid and thyroid hormone receptor (SMART) and HDAC3 to silence Xi. Right, Mhrt prevents SWI/SNF binding to corresponding DNA loci.<br />
<br />
LncRNA (Xist) annotations:<br />
* MF: GO:0030674 protein-macromolecule adaptor activity + appropriate information (eg part_of GO:0006338 chromatin remodeling)<br />
* BP: GO:0006338 chromatin remodeling<br />
<br />
LncRNA (Mhrt) annotations based on [[https://pubmed.ncbi.nlm.nih.gov/25119045/ PMID:25119045]]:<br />
* MF: GO:0140311 protein sequestering activity + appropriate information etc (eg has_inputs Brg1/Smarca4, Q3TKT4), part_of GO:0006338 chromatin remodeling)<br />
* BP: GO:0006338 chromatin remodeling<br />
<br />
=== Triplex-Mediated Changes in Chromatin Structure ===<br />
<br />
Figure 2f, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: Khps1 enhances Pol II transcription by forming an R-loop that anchors Khps1-interacting p300/CBP to the SPHK1 promoter.<br />
<br />
LncRNA (Khps1) annotations based on [[https://pubmed.ncbi.nlm.nih.gov/26590717/ PMID: 26590717]]:<br />
<br />
* MF: GO:0030674 protein-macromolecule adaptor activity or GO:0001010 RNA polymerase II sequence-specific DNA-binding transcription factor recruiting activity + appropriate information etc (eg part_of GO:0045944 positive regulation of transcription by RNA polymerase II)<br />
* MF: GO:1990837 sequence-specific double-stranded DNA binding + appropriate information etc (eg part_of GO:0006325 chromatin organization)<br />
* BP: GO:0006325 chromatin organization<br />
* BP: GO:0045944 positive regulation of transcription by RNA polymerase II<br />
<br />
=== RNA polymerase inhibitor activity ===<br />
<br />
Figure 2g, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]:lncRNAs interfere with Pol II transcription machineries both at the initiation (left) and elongation (right) stages.<br />
<br />
LncRNA annotations:<br />
* MF: GO:0140870 RNA polymerase inhibitor activity<br />
* BP:GO:0000122 negative regulation of transcription by RNA polymerase II<br />
<br />
=== repressor of RNA polymerase inhibitor activity ===<br />
<br />
Figure 2h, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: SLERT promotes Pol I transcription by binding DDX21 to alter its conformation, thereby releasing its inhibitory effect on Pol I.<br />
<br />
LncRNA (SLERT) annotations:<br />
* MF: GO:0140871 repressor of RNA polymerase inhibitor activity + appropriate information (eg has_input DDX21)<br />
* BP: GO:0045943 positive regulation of transcription by RNA polymerase I<br />
<br />
=== molecular condensate scaffold activity ===<br />
<br />
Figure 2i, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: NEAT1 is an architectural lncRNA that nucleates paraspeckles. Upon cellular stress, altered NEAT1 transcription and processing lead to changes of paraspeckles. PSP, paraspeckle proteins.<br />
<br />
LncRNA (NEAT1) annotations:<br />
* MF: GO:0140693 molecular condensate scaffold activity + additional information (eg part_of GO:0006325 chromatin organization or GO:0006996 organelle organization)<br />
* BP: GO:0030575 nuclear body organization<br />
<br />
=== miRNA inhibitor activity ===<br />
<br />
See decision tree above <br />
Figure 2k, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]:Cyrano, harbouring miR-7 binding site and mediates its destruction by target-RNA-directed miRNA degradation.<br />
<br />
<br />
LncRNA Cyrano annotations e.g. mouse, URS000075A502_10090, URS000075B8A8_10090 [[https://pubmed.ncbi.nlm.nih.gov/29887379/ PMID:29887379]]. A Network of Noncoding Regulatory RNAs Acts in the Mammalian Brain. (2018)<br />
* MF GO:0140869 miRNA inhibitor activity via base-pairing<br />
** has_input URS0000591950_10090 (miR-7b-5p)& URS000075DE8D_10090 (miR-7a-5p) <br />
* BP: GO:0000512 lncRNA-mediated post-transcriptional gene silencing<br />
* BP: GO:0140958 target-directed miRNA degradation<br />
<br />
Note that the level of Cyrano does not change but the level of target miR-7 is down-regulated dramatically, as the lncRNA is not destroyed in the process. If the lncRNA decreases with the miRNA, then it is not target-directed miRNA degradation, but can be annotated with another more appropriate term such as GO:0010587 miRNA catabolic process.<br />
<br />
=== mRNA degradation ===<br />
<br />
Figure 2l, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: lncRNAs modulate mRNA stability by associating with proteins involved in mRNA degradation. Left, double-stranded RNAs formed by Alu-containing lncRNAs with mRNA 3′ UTRs recruit STAU1 to induce STAU1-mediated mRNA decay (SMD). Right, NORAD stabilizes PUMILIO 1/2 (PUM1/2)-targeted mRNAs via sequestering PUM1/2 from mRNAs.<br />
<br />
LncRNA (NORAD) annotations:<br />
* MF: GO:1903231 mRNA base-pairing translational repressor activity + additional information (eg part_of GO:0000512 lncRNA-mediated post-transcriptional gene silencing)<br />
* BP: GO:0000512 lncRNA-mediated post-transcriptional gene silencing<br />
<br />
=== mRNA translation repression ===<br />
<br />
Figure 2m, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: lncRNAs regulate translation. Association of lincRNA-p21 (linc-p21) with HuR favours the recruitment of let-7/Ago2, leading to its destabilization. In the absence of HuR, lincRNA-p21 identifies mRNA targets to repress their translation by recruiting the translation repressor Rck129. RISC, RNA-induced silencing complex.<br />
<br />
LncRNA annotations:<br />
* MF: GO:1903231 mRNA base-pairing translational repressor activity + additional information (eg part_of GO:0000512 lncRNA-mediated post-transcriptional gene silencing)<br />
* BP: GO:0000512 lncRNA-mediated post-transcriptional gene silencing<br />
<br />
=== regulation of post-translational modifications ===<br />
<br />
Figure 2n, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: lncRNAs modulate post-translational modifications. Lnc-DC directly interacts with STAT3 to prevent its dephosphorylation by SHP1 (PTPN6).<br />
<br />
<br />
LncRNA annotations URS00007B42BD_9606 (GenBank:KJ020271) and URS00007B3652_9606 (GenBank:KJ020272) from [[https://pubmed.ncbi.nlm.nih.gov/24744378/ PMID:24744378]] 'The STAT3-binding long noncoding RNA lnc-DC controls human dendritic cell differentiation'.<br />
* MF: GO:0019212 phosphatase inhibitor activity<br />
**has_input UniProtKB:P29350 (PTPN6)<br />
* MF: GO:0097677 STAT family protein binding<br />
**has_input UniProtKB:P40763 (STAT3)<br />
<br />
BP terms to describe regulation of pathway and involvement in processes:<br />
* BP: GO:0046427 positive regulation of receptor signaling pathway via JAK-STAT<br />
* BP: GO0097028 dendritic cell differentiation<br />
<br />
<br />
[[Category:Annotation Guidelines]]</div>Hla28https://wiki.geneontology.org/index.php?title=LncRNA_GO_annotation_manual&diff=86641LncRNA GO annotation manual2024-03-06T22:08:36Z<p>Hla28: /* Random inactivation of X chromosome */</p>
<hr />
<div>LncRNAs have multiple and varied activities (see [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]] which describes 13 roles of lncRNAs), these guidelines are suggestions for the curation of some of these lncRNAs. These were discussed [https://github.com/geneontology/go-ontology/issues/23028 here].<br />
<br />
===Decision tree to assist with curation of lncRNA:miRNA interactions===<br />
<br />
These guidelines are for the curation of lncRNAs that bind to miRNA and prevent miRNA activity. These lncRNAs are often described as sponge lncRNAs.<br />
<br />
Link to LncRNA_Decision_Tree pdf[[https://wiki.geneontology.org/images/e/e4/LncRNA_Decision_Tree.pdf]]<br />
<br />
[[File:LncRNA Decision Tree.jpg|960x540px]]<br />
<br />
'''Decision Tree for the GO terms and annotation extensions used for capturing targets of lncRNAs.''' The types of evidence in the blue boxes are described further in the text. Information about the cell or tissue that the interaction occurs in can be captured for example in the annotation extension field using: occurs_in (insert cell ontology ID and/or UBERON ID based on cell and/or tissue type respectively). This information can be included when inhibition of the lncRNA leads to an increase in the endogenous miRNA (or decrease in the miRNA target protein level). Slightly weaker evidence to support inclusion of the cell or tissue information would be evidence that the lncRNA is expressed in these cells/this tissue AND that the authors are confident that the lncRNA target is also being regulated in these cells/this tissue. For example, when the addition of the lncRNA leads to a decrease in the endogenous miRNA or increase in the endogenous protein level.<br />
<br />
'''Note:''' to be able to indicate any target in a GO annotation, the prediction evidence does not need to be in the paper you are annotating, it could be from another paper or a prediction database. When looking at predictions or validations in a prediction database, it is recommended to check the references cited for the target as they may serve as a good source of experimental annotation. Additionally, it has been found that some of the cited papers do not support the validation of the targets. Annotations to “miRNA inhibitor activity via base pairing” (GO:0140869) should ONLY be made from the paper containing the experimental evidence, however it is acceptable to indicate in the annotation extension of a “gene silencing by miRNA” annotation that the target of gene silencing is direct (by using ''has_input'') if the evidence for binding is in another paper.<br />
<br />
===Random inactivation of X chromosome===<br />
<br />
Figure 2b [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: Xist modulates inactive X chromosome (Xi) architecture during X chromosome inactivation (XCI) by recruiting Xi to associate with the lamin B receptor (LBR) at the nuclear lamina to silence transcription.<br />
<br />
LncRNA (Xist) Annotations:<br />
* MF: GO:0140463 chromatin-protein adaptor activity<br />
* BF: GO:0060816 random inactivation of X chromosome<br />
<br />
=== DNA-DNA tethering activity ===<br />
<br />
Figure 2c [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: Firre transcripts localize to their transcription site and five additional autosomal chromosomal loci in trans to affect interactions between distant genomic regions.<br />
<br />
LncRNA (Firre) annotations:<br />
* MF: GO:0106260 DNA-DNA tethering activity + appropriate information etc (eg part_of GO:0006325 chromatin organization)<br />
* BP: GO:0006325 chromatin organization<br />
<br />
=== Promoter-enhancer loop anchoring activity ===<br />
<br />
Figure 2d [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: CCAT1-L accumulates in cis to modulate chromatin loops between enhancers and the promoter of MYC.<br />
<br />
LncRNA (CCAT1-L) annotations:<br />
* MF: GO:0140585 promoter-enhancer loop anchoring activity + appropriate information etc (eg part_of GO:0140588 chromatin looping)<br />
* BP: GO:0140588 chromatin looping<br />
<br />
=== Regulation of chromatin accessibility ===<br />
<br />
Figure 2e [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: lncRNAs regulate chromatin accessibility. Left, Xist recruits HDAC1-associated repressor protein (SHARP), silencing the mediator for retinoid and thyroid hormone receptor (SMART) and HDAC3 to silence Xi. Right, Mhrt prevents SWI/SNF binding to corresponding DNA loci.<br />
<br />
LncRNA (Xist) annotations:<br />
* MF: GO:0030674 protein-macromolecule adaptor activity + appropriate information (eg part_of GO:0006338 chromatin remodeling)<br />
* BP: GO:0006338 chromatin remodeling<br />
<br />
LncRNA (Mhrt) annotations based on [[https://pubmed.ncbi.nlm.nih.gov/25119045/ PMID:25119045]]:<br />
* MF: GO:0140311 protein sequestering activity + appropriate information etc (eg has_inputs Brg1/Smarca4, Q3TKT4), part_of GO:0006338 chromatin remodeling)<br />
* BP: GO:0006338 chromatin remodeling<br />
<br />
=== Triplex-Mediated Changes in Chromatin Structure ===<br />
<br />
Figure 2f, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: Khps1 enhances Pol II transcription by forming an R-loop that anchors Khps1-interacting p300/CBP to the SPHK1 promoter.<br />
<br />
LncRNA (Khps1) annotations based on [[https://pubmed.ncbi.nlm.nih.gov/26590717/ PMID: 26590717]]:<br />
<br />
* MF: GO:0030674 protein-macromolecule adaptor activity or GO:0001010 RNA polymerase II sequence-specific DNA-binding transcription factor recruiting activity + appropriate information etc (eg part_of GO:0045944 positive regulation of transcription by RNA polymerase II)<br />
* MF: GO:1990837 sequence-specific double-stranded DNA binding + appropriate information etc (eg part_of GO:0006325 chromatin organization)<br />
* BP: GO:0006325 chromatin organization<br />
* BP: GO:0045944 positive regulation of transcription by RNA polymerase II<br />
<br />
=== RNA polymerase inhibitor activity ===<br />
<br />
Figure 2g, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]:lncRNAs interfere with Pol II transcription machineries both at the initiation (left) and elongation (right) stages.<br />
<br />
LncRNA annotations:<br />
* MF: GO:0140870 RNA polymerase inhibitor activity<br />
* BP:GO:0000122 negative regulation of transcription by RNA polymerase II<br />
<br />
=== repressor of RNA polymerase inhibitor activity ===<br />
<br />
Figure 2h, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: SLERT promotes Pol I transcription by binding DDX21 to alter its conformation, thereby releasing its inhibitory effect on Pol I.<br />
<br />
LncRNA (SLERT) annotations:<br />
* MF: GO:0140871 repressor of RNA polymerase inhibitor activity + appropriate information (eg has_input DDX21)<br />
* BP: GO:0045943 positive regulation of transcription by RNA polymerase I<br />
<br />
=== molecular condensate scaffold activity ===<br />
<br />
Figure 2i, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: NEAT1 is an architectural lncRNA that nucleates paraspeckles. Upon cellular stress, altered NEAT1 transcription and processing lead to changes of paraspeckles. PSP, paraspeckle proteins.<br />
<br />
LncRNA (NEAT1) annotations:<br />
* MF: GO:0140693 molecular condensate scaffold activity + additional information (eg part_of GO:0006325 chromatin organization or GO:0006996 organelle organization)<br />
* BP: GO:0030575 nuclear body organization<br />
<br />
=== miRNA inhibitor activity ===<br />
<br />
See decision tree above <br />
Figure 2k, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]:Cyrano, harbouring miR-7 binding site and mediates its destruction by target-RNA-directed miRNA degradation.<br />
<br />
<br />
LncRNA Cyrano annotations e.g. mouse, URS000075A502_10090, URS000075B8A8_10090 [[https://pubmed.ncbi.nlm.nih.gov/29887379/ PMID:29887379]]. A Network of Noncoding Regulatory RNAs Acts in the Mammalian Brain. (2018)<br />
* MF GO:0140869 miRNA inhibitor activity via base-pairing<br />
** has_input URS0000591950_10090 (miR-7b-5p)& URS000075DE8D_10090 (miR-7a-5p) <br />
* BP: GO:0000512 lncRNA-mediated post-transcriptional gene silencing<br />
* BP: GO:0140958 target-directed miRNA degradation<br />
<br />
Note that the level of Cyrano does not change but the level of target miR-7 is down-regulated dramatically, as the lncRNA is not destroyed in the process. If the lncRNA decreases with the miRNA, then it is not target-directed miRNA degradation, but can be annotated with another more appropriate term such as GO:0010587 miRNA catabolic process.<br />
<br />
=== mRNA degradation ===<br />
<br />
Figure 2l, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: lncRNAs modulate mRNA stability by associating with proteins involved in mRNA degradation. Left, double-stranded RNAs formed by Alu-containing lncRNAs with mRNA 3′ UTRs recruit STAU1 to induce STAU1-mediated mRNA decay (SMD). Right, NORAD stabilizes PUMILIO 1/2 (PUM1/2)-targeted mRNAs via sequestering PUM1/2 from mRNAs.<br />
<br />
LncRNA (NORAD) annotations:<br />
* MF: GO:1903231 mRNA base-pairing translational repressor activity + additional information (eg part_of GO:0000512 lncRNA-mediated post-transcriptional gene silencing)<br />
* BP: GO:0000512 lncRNA-mediated post-transcriptional gene silencing<br />
<br />
=== mRNA translation repression ===<br />
<br />
Figure 2m, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: lncRNAs regulate translation. Association of lincRNA-p21 (linc-p21) with HuR favours the recruitment of let-7/Ago2, leading to its destabilization. In the absence of HuR, lincRNA-p21 identifies mRNA targets to repress their translation by recruiting the translation repressor Rck129. RISC, RNA-induced silencing complex.<br />
<br />
LncRNA annotations:<br />
* MF: GO:1903231 mRNA base-pairing translational repressor activity + additional information (eg part_of GO:0000512 lncRNA-mediated post-transcriptional gene silencing)<br />
* BP: GO:0000512 lncRNA-mediated post-transcriptional gene silencing<br />
<br />
=== regulation of post-translational modifications ===<br />
<br />
Figure 2n, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: lncRNAs modulate post-translational modifications. Lnc-DC directly interacts with STAT3 to prevent its dephosphorylation by SHP1 (PTPN6).<br />
<br />
<br />
LncRNA annotations URS00007B42BD_9606 (GenBank:KJ020271) and URS00007B3652_9606 (GenBank:KJ020272) from [[https://pubmed.ncbi.nlm.nih.gov/24744378/ PMID:24744378]] 'The STAT3-binding long noncoding RNA lnc-DC controls human dendritic cell differentiation'.<br />
* MF: GO:0019212 phosphatase inhibitor activity<br />
**has_input UniProtKB:P29350 (PTPN6)<br />
* MF: GO:0097677 STAT family protein binding<br />
**has_input UniProtKB:P40763 (STAT3)<br />
<br />
BP terms to describe regulation of pathway and involvement in processes:<br />
* BP: GO:0046427 positive regulation of receptor signaling pathway via JAK-STAT<br />
* BP: GO0097028 dendritic cell differentiation<br />
<br />
<br />
[[Category:Annotation Guidelines]]</div>Hla28https://wiki.geneontology.org/index.php?title=LncRNA_GO_annotation_manual&diff=86640LncRNA GO annotation manual2024-03-06T22:04:42Z<p>Hla28: /* Regulation of post-translational modifications */</p>
<hr />
<div>LncRNAs have multiple and varied activities (see [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]] which describes 13 roles of lncRNAs), these guidelines are suggestions for the curation of some of these lncRNAs. These were discussed [https://github.com/geneontology/go-ontology/issues/23028 here].<br />
<br />
===Decision tree to assist with curation of lncRNA:miRNA interactions===<br />
<br />
These guidelines are for the curation of lncRNAs that bind to miRNA and prevent miRNA activity. These lncRNAs are often described as sponge lncRNAs.<br />
<br />
Link to LncRNA_Decision_Tree pdf[[https://wiki.geneontology.org/images/e/e4/LncRNA_Decision_Tree.pdf]]<br />
<br />
[[File:LncRNA Decision Tree.jpg|960x540px]]<br />
<br />
'''Decision Tree for the GO terms and annotation extensions used for capturing targets of lncRNAs.''' The types of evidence in the blue boxes are described further in the text. Information about the cell or tissue that the interaction occurs in can be captured for example in the annotation extension field using: occurs_in (insert cell ontology ID and/or UBERON ID based on cell and/or tissue type respectively). This information can be included when inhibition of the lncRNA leads to an increase in the endogenous miRNA (or decrease in the miRNA target protein level). Slightly weaker evidence to support inclusion of the cell or tissue information would be evidence that the lncRNA is expressed in these cells/this tissue AND that the authors are confident that the lncRNA target is also being regulated in these cells/this tissue. For example, when the addition of the lncRNA leads to a decrease in the endogenous miRNA or increase in the endogenous protein level.<br />
<br />
'''Note:''' to be able to indicate any target in a GO annotation, the prediction evidence does not need to be in the paper you are annotating, it could be from another paper or a prediction database. When looking at predictions or validations in a prediction database, it is recommended to check the references cited for the target as they may serve as a good source of experimental annotation. Additionally, it has been found that some of the cited papers do not support the validation of the targets. Annotations to “miRNA inhibitor activity via base pairing” (GO:0140869) should ONLY be made from the paper containing the experimental evidence, however it is acceptable to indicate in the annotation extension of a “gene silencing by miRNA” annotation that the target of gene silencing is direct (by using ''has_input'') if the evidence for binding is in another paper.<br />
<br />
===Random inactivation of X chromosome===<br />
<br />
Figure 2b [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: Xist modulates inactive X chromosome (Xi) architecture during X chromosome inactivation (XCI) by recruiting Xi to associate with the lamin B receptor (LBR) at the nuclear lamina to silence transcription.<br />
<br />
LncRNA (Xist) Annotations:<br />
* MF: GO:0140463 chromatin-protein adaptor activity + appropriate information etc (eg part_of GO:0060820 inactivation of X chromosome by heterochromatin formation)<br />
* BF: GO:0060816 random inactivation of X chromosome<br />
<br />
=== DNA-DNA tethering activity ===<br />
<br />
Figure 2c [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: Firre transcripts localize to their transcription site and five additional autosomal chromosomal loci in trans to affect interactions between distant genomic regions.<br />
<br />
LncRNA (Firre) annotations:<br />
* MF: GO:0106260 DNA-DNA tethering activity + appropriate information etc (eg part_of GO:0006325 chromatin organization)<br />
* BP: GO:0006325 chromatin organization<br />
<br />
=== Promoter-enhancer loop anchoring activity ===<br />
<br />
Figure 2d [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: CCAT1-L accumulates in cis to modulate chromatin loops between enhancers and the promoter of MYC.<br />
<br />
LncRNA (CCAT1-L) annotations:<br />
* MF: GO:0140585 promoter-enhancer loop anchoring activity + appropriate information etc (eg part_of GO:0140588 chromatin looping)<br />
* BP: GO:0140588 chromatin looping<br />
<br />
=== Regulation of chromatin accessibility ===<br />
<br />
Figure 2e [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: lncRNAs regulate chromatin accessibility. Left, Xist recruits HDAC1-associated repressor protein (SHARP), silencing the mediator for retinoid and thyroid hormone receptor (SMART) and HDAC3 to silence Xi. Right, Mhrt prevents SWI/SNF binding to corresponding DNA loci.<br />
<br />
LncRNA (Xist) annotations:<br />
* MF: GO:0030674 protein-macromolecule adaptor activity + appropriate information (eg part_of GO:0006338 chromatin remodeling)<br />
* BP: GO:0006338 chromatin remodeling<br />
<br />
LncRNA (Mhrt) annotations based on [[https://pubmed.ncbi.nlm.nih.gov/25119045/ PMID:25119045]]:<br />
* MF: GO:0140311 protein sequestering activity + appropriate information etc (eg has_inputs Brg1/Smarca4, Q3TKT4), part_of GO:0006338 chromatin remodeling)<br />
* BP: GO:0006338 chromatin remodeling<br />
<br />
=== Triplex-Mediated Changes in Chromatin Structure ===<br />
<br />
Figure 2f, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: Khps1 enhances Pol II transcription by forming an R-loop that anchors Khps1-interacting p300/CBP to the SPHK1 promoter.<br />
<br />
LncRNA (Khps1) annotations based on [[https://pubmed.ncbi.nlm.nih.gov/26590717/ PMID: 26590717]]:<br />
<br />
* MF: GO:0030674 protein-macromolecule adaptor activity or GO:0001010 RNA polymerase II sequence-specific DNA-binding transcription factor recruiting activity + appropriate information etc (eg part_of GO:0045944 positive regulation of transcription by RNA polymerase II)<br />
* MF: GO:1990837 sequence-specific double-stranded DNA binding + appropriate information etc (eg part_of GO:0006325 chromatin organization)<br />
* BP: GO:0006325 chromatin organization<br />
* BP: GO:0045944 positive regulation of transcription by RNA polymerase II<br />
<br />
=== RNA polymerase inhibitor activity ===<br />
<br />
Figure 2g, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]:lncRNAs interfere with Pol II transcription machineries both at the initiation (left) and elongation (right) stages.<br />
<br />
LncRNA annotations:<br />
* MF: GO:0140870 RNA polymerase inhibitor activity<br />
* BP:GO:0000122 negative regulation of transcription by RNA polymerase II<br />
<br />
=== repressor of RNA polymerase inhibitor activity ===<br />
<br />
Figure 2h, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: SLERT promotes Pol I transcription by binding DDX21 to alter its conformation, thereby releasing its inhibitory effect on Pol I.<br />
<br />
LncRNA (SLERT) annotations:<br />
* MF: GO:0140871 repressor of RNA polymerase inhibitor activity + appropriate information (eg has_input DDX21)<br />
* BP: GO:0045943 positive regulation of transcription by RNA polymerase I<br />
<br />
=== molecular condensate scaffold activity ===<br />
<br />
Figure 2i, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: NEAT1 is an architectural lncRNA that nucleates paraspeckles. Upon cellular stress, altered NEAT1 transcription and processing lead to changes of paraspeckles. PSP, paraspeckle proteins.<br />
<br />
LncRNA (NEAT1) annotations:<br />
* MF: GO:0140693 molecular condensate scaffold activity + additional information (eg part_of GO:0006325 chromatin organization or GO:0006996 organelle organization)<br />
* BP: GO:0030575 nuclear body organization<br />
<br />
=== miRNA inhibitor activity ===<br />
<br />
See decision tree above <br />
Figure 2k, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]:Cyrano, harbouring miR-7 binding site and mediates its destruction by target-RNA-directed miRNA degradation.<br />
<br />
<br />
LncRNA Cyrano annotations e.g. mouse, URS000075A502_10090, URS000075B8A8_10090 [[https://pubmed.ncbi.nlm.nih.gov/29887379/ PMID:29887379]]. A Network of Noncoding Regulatory RNAs Acts in the Mammalian Brain. (2018)<br />
* MF GO:0140869 miRNA inhibitor activity via base-pairing<br />
** has_input URS0000591950_10090 (miR-7b-5p)& URS000075DE8D_10090 (miR-7a-5p) <br />
* BP: GO:0000512 lncRNA-mediated post-transcriptional gene silencing<br />
* BP: GO:0140958 target-directed miRNA degradation<br />
<br />
Note that the level of Cyrano does not change but the level of target miR-7 is down-regulated dramatically, as the lncRNA is not destroyed in the process. If the lncRNA decreases with the miRNA, then it is not target-directed miRNA degradation, but can be annotated with another more appropriate term such as GO:0010587 miRNA catabolic process.<br />
<br />
=== mRNA degradation ===<br />
<br />
Figure 2l, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: lncRNAs modulate mRNA stability by associating with proteins involved in mRNA degradation. Left, double-stranded RNAs formed by Alu-containing lncRNAs with mRNA 3′ UTRs recruit STAU1 to induce STAU1-mediated mRNA decay (SMD). Right, NORAD stabilizes PUMILIO 1/2 (PUM1/2)-targeted mRNAs via sequestering PUM1/2 from mRNAs.<br />
<br />
LncRNA (NORAD) annotations:<br />
* MF: GO:1903231 mRNA base-pairing translational repressor activity + additional information (eg part_of GO:0000512 lncRNA-mediated post-transcriptional gene silencing)<br />
* BP: GO:0000512 lncRNA-mediated post-transcriptional gene silencing<br />
<br />
=== mRNA translation repression ===<br />
<br />
Figure 2m, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: lncRNAs regulate translation. Association of lincRNA-p21 (linc-p21) with HuR favours the recruitment of let-7/Ago2, leading to its destabilization. In the absence of HuR, lincRNA-p21 identifies mRNA targets to repress their translation by recruiting the translation repressor Rck129. RISC, RNA-induced silencing complex.<br />
<br />
LncRNA annotations:<br />
* MF: GO:1903231 mRNA base-pairing translational repressor activity + additional information (eg part_of GO:0000512 lncRNA-mediated post-transcriptional gene silencing)<br />
* BP: GO:0000512 lncRNA-mediated post-transcriptional gene silencing<br />
<br />
=== regulation of post-translational modifications ===<br />
<br />
Figure 2n, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: lncRNAs modulate post-translational modifications. Lnc-DC directly interacts with STAT3 to prevent its dephosphorylation by SHP1 (PTPN6).<br />
<br />
<br />
LncRNA annotations URS00007B42BD_9606 (GenBank:KJ020271) and URS00007B3652_9606 (GenBank:KJ020272) from [[https://pubmed.ncbi.nlm.nih.gov/24744378/ PMID:24744378]] 'The STAT3-binding long noncoding RNA lnc-DC controls human dendritic cell differentiation'.<br />
* MF: GO:0019212 phosphatase inhibitor activity<br />
**has_input UniProtKB:P29350 (PTPN6)<br />
* MF: GO:0097677 STAT family protein binding<br />
**has_input UniProtKB:P40763 (STAT3)<br />
<br />
BP terms to describe regulation of pathway and involvement in processes:<br />
* BP: GO:0046427 positive regulation of receptor signaling pathway via JAK-STAT<br />
* BP: GO0097028 dendritic cell differentiation<br />
<br />
<br />
[[Category:Annotation Guidelines]]</div>Hla28https://wiki.geneontology.org/index.php?title=LncRNA_GO_annotation_manual&diff=86639LncRNA GO annotation manual2024-03-06T22:03:21Z<p>Hla28: /* regulation of post-translational modifications */</p>
<hr />
<div>LncRNAs have multiple and varied activities (see [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]] which describes 13 roles of lncRNAs), these guidelines are suggestions for the curation of some of these lncRNAs. These were discussed [https://github.com/geneontology/go-ontology/issues/23028 here].<br />
<br />
===Decision tree to assist with curation of lncRNA:miRNA interactions===<br />
<br />
These guidelines are for the curation of lncRNAs that bind to miRNA and prevent miRNA activity. These lncRNAs are often described as sponge lncRNAs.<br />
<br />
Link to LncRNA_Decision_Tree pdf[[https://wiki.geneontology.org/images/e/e4/LncRNA_Decision_Tree.pdf]]<br />
<br />
[[File:LncRNA Decision Tree.jpg|960x540px]]<br />
<br />
'''Decision Tree for the GO terms and annotation extensions used for capturing targets of lncRNAs.''' The types of evidence in the blue boxes are described further in the text. Information about the cell or tissue that the interaction occurs in can be captured for example in the annotation extension field using: occurs_in (insert cell ontology ID and/or UBERON ID based on cell and/or tissue type respectively). This information can be included when inhibition of the lncRNA leads to an increase in the endogenous miRNA (or decrease in the miRNA target protein level). Slightly weaker evidence to support inclusion of the cell or tissue information would be evidence that the lncRNA is expressed in these cells/this tissue AND that the authors are confident that the lncRNA target is also being regulated in these cells/this tissue. For example, when the addition of the lncRNA leads to a decrease in the endogenous miRNA or increase in the endogenous protein level.<br />
<br />
'''Note:''' to be able to indicate any target in a GO annotation, the prediction evidence does not need to be in the paper you are annotating, it could be from another paper or a prediction database. When looking at predictions or validations in a prediction database, it is recommended to check the references cited for the target as they may serve as a good source of experimental annotation. Additionally, it has been found that some of the cited papers do not support the validation of the targets. Annotations to “miRNA inhibitor activity via base pairing” (GO:0140869) should ONLY be made from the paper containing the experimental evidence, however it is acceptable to indicate in the annotation extension of a “gene silencing by miRNA” annotation that the target of gene silencing is direct (by using ''has_input'') if the evidence for binding is in another paper.<br />
<br />
===Random inactivation of X chromosome===<br />
<br />
Figure 2b [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: Xist modulates inactive X chromosome (Xi) architecture during X chromosome inactivation (XCI) by recruiting Xi to associate with the lamin B receptor (LBR) at the nuclear lamina to silence transcription.<br />
<br />
LncRNA (Xist) Annotations:<br />
* MF: GO:0140463 chromatin-protein adaptor activity + appropriate information etc (eg part_of GO:0060820 inactivation of X chromosome by heterochromatin formation)<br />
* BF: GO:0060816 random inactivation of X chromosome<br />
<br />
=== DNA-DNA tethering activity ===<br />
<br />
Figure 2c [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: Firre transcripts localize to their transcription site and five additional autosomal chromosomal loci in trans to affect interactions between distant genomic regions.<br />
<br />
LncRNA (Firre) annotations:<br />
* MF: GO:0106260 DNA-DNA tethering activity + appropriate information etc (eg part_of GO:0006325 chromatin organization)<br />
* BP: GO:0006325 chromatin organization<br />
<br />
=== Promoter-enhancer loop anchoring activity ===<br />
<br />
Figure 2d [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: CCAT1-L accumulates in cis to modulate chromatin loops between enhancers and the promoter of MYC.<br />
<br />
LncRNA (CCAT1-L) annotations:<br />
* MF: GO:0140585 promoter-enhancer loop anchoring activity + appropriate information etc (eg part_of GO:0140588 chromatin looping)<br />
* BP: GO:0140588 chromatin looping<br />
<br />
=== Regulation of chromatin accessibility ===<br />
<br />
Figure 2e [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: lncRNAs regulate chromatin accessibility. Left, Xist recruits HDAC1-associated repressor protein (SHARP), silencing the mediator for retinoid and thyroid hormone receptor (SMART) and HDAC3 to silence Xi. Right, Mhrt prevents SWI/SNF binding to corresponding DNA loci.<br />
<br />
LncRNA (Xist) annotations:<br />
* MF: GO:0030674 protein-macromolecule adaptor activity + appropriate information (eg part_of GO:0006338 chromatin remodeling)<br />
* BP: GO:0006338 chromatin remodeling<br />
<br />
LncRNA (Mhrt) annotations based on [[https://pubmed.ncbi.nlm.nih.gov/25119045/ PMID:25119045]]:<br />
* MF: GO:0140311 protein sequestering activity + appropriate information etc (eg has_inputs Brg1/Smarca4, Q3TKT4), part_of GO:0006338 chromatin remodeling)<br />
* BP: GO:0006338 chromatin remodeling<br />
<br />
=== Triplex-Mediated Changes in Chromatin Structure ===<br />
<br />
Figure 2f, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: Khps1 enhances Pol II transcription by forming an R-loop that anchors Khps1-interacting p300/CBP to the SPHK1 promoter.<br />
<br />
LncRNA (Khps1) annotations based on [[https://pubmed.ncbi.nlm.nih.gov/26590717/ PMID: 26590717]]:<br />
<br />
* MF: GO:0030674 protein-macromolecule adaptor activity or GO:0001010 RNA polymerase II sequence-specific DNA-binding transcription factor recruiting activity + appropriate information etc (eg part_of GO:0045944 positive regulation of transcription by RNA polymerase II)<br />
* MF: GO:1990837 sequence-specific double-stranded DNA binding + appropriate information etc (eg part_of GO:0006325 chromatin organization)<br />
* BP: GO:0006325 chromatin organization<br />
* BP: GO:0045944 positive regulation of transcription by RNA polymerase II<br />
<br />
=== RNA polymerase inhibitor activity ===<br />
<br />
Figure 2g, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]:lncRNAs interfere with Pol II transcription machineries both at the initiation (left) and elongation (right) stages.<br />
<br />
LncRNA annotations:<br />
* MF: GO:0140870 RNA polymerase inhibitor activity<br />
* BP:GO:0000122 negative regulation of transcription by RNA polymerase II<br />
<br />
=== repressor of RNA polymerase inhibitor activity ===<br />
<br />
Figure 2h, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: SLERT promotes Pol I transcription by binding DDX21 to alter its conformation, thereby releasing its inhibitory effect on Pol I.<br />
<br />
LncRNA (SLERT) annotations:<br />
* MF: GO:0140871 repressor of RNA polymerase inhibitor activity + appropriate information (eg has_input DDX21)<br />
* BP: GO:0045943 positive regulation of transcription by RNA polymerase I<br />
<br />
=== molecular condensate scaffold activity ===<br />
<br />
Figure 2i, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: NEAT1 is an architectural lncRNA that nucleates paraspeckles. Upon cellular stress, altered NEAT1 transcription and processing lead to changes of paraspeckles. PSP, paraspeckle proteins.<br />
<br />
LncRNA (NEAT1) annotations:<br />
* MF: GO:0140693 molecular condensate scaffold activity + additional information (eg part_of GO:0006325 chromatin organization or GO:0006996 organelle organization)<br />
* BP: GO:0030575 nuclear body organization<br />
<br />
=== miRNA inhibitor activity ===<br />
<br />
See decision tree above <br />
Figure 2k, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]:Cyrano, harbouring miR-7 binding site and mediates its destruction by target-RNA-directed miRNA degradation.<br />
<br />
<br />
LncRNA Cyrano annotations e.g. mouse, URS000075A502_10090, URS000075B8A8_10090 [[https://pubmed.ncbi.nlm.nih.gov/29887379/ PMID:29887379]]. A Network of Noncoding Regulatory RNAs Acts in the Mammalian Brain. (2018)<br />
* MF GO:0140869 miRNA inhibitor activity via base-pairing<br />
** has_input URS0000591950_10090 (miR-7b-5p)& URS000075DE8D_10090 (miR-7a-5p) <br />
* BP: GO:0000512 lncRNA-mediated post-transcriptional gene silencing<br />
* BP: GO:0140958 target-directed miRNA degradation<br />
<br />
Note that the level of Cyrano does not change but the level of target miR-7 is down-regulated dramatically, as the lncRNA is not destroyed in the process. If the lncRNA decreases with the miRNA, then it is not target-directed miRNA degradation, but can be annotated with another more appropriate term such as GO:0010587 miRNA catabolic process.<br />
<br />
=== mRNA degradation ===<br />
<br />
Figure 2l, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: lncRNAs modulate mRNA stability by associating with proteins involved in mRNA degradation. Left, double-stranded RNAs formed by Alu-containing lncRNAs with mRNA 3′ UTRs recruit STAU1 to induce STAU1-mediated mRNA decay (SMD). Right, NORAD stabilizes PUMILIO 1/2 (PUM1/2)-targeted mRNAs via sequestering PUM1/2 from mRNAs.<br />
<br />
LncRNA (NORAD) annotations:<br />
* MF: GO:1903231 mRNA base-pairing translational repressor activity + additional information (eg part_of GO:0000512 lncRNA-mediated post-transcriptional gene silencing)<br />
* BP: GO:0000512 lncRNA-mediated post-transcriptional gene silencing<br />
<br />
=== mRNA translation repression ===<br />
<br />
Figure 2m, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: lncRNAs regulate translation. Association of lincRNA-p21 (linc-p21) with HuR favours the recruitment of let-7/Ago2, leading to its destabilization. In the absence of HuR, lincRNA-p21 identifies mRNA targets to repress their translation by recruiting the translation repressor Rck129. RISC, RNA-induced silencing complex.<br />
<br />
LncRNA annotations:<br />
* MF: GO:1903231 mRNA base-pairing translational repressor activity + additional information (eg part_of GO:0000512 lncRNA-mediated post-transcriptional gene silencing)<br />
* BP: GO:0000512 lncRNA-mediated post-transcriptional gene silencing<br />
<br />
=== Regulation of post-translational modifications ===<br />
<br />
Figure 2n, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: lncRNAs modulate post-translational modifications. Lnc-DC directly interacts with STAT3 to prevent its dephosphorylation by SHP1 (PTPN6).<br />
<br />
<br />
LncRNA annotations URS00007B42BD_9606 (GenBank:KJ020271) and URS00007B3652_9606 (GenBank:KJ020272) from [[https://pubmed.ncbi.nlm.nih.gov/24744378/ PMID:24744378]] 'The STAT3-binding long noncoding RNA lnc-DC controls human dendritic cell differentiation'.<br />
* MF: GO:0019212 phosphatase inhibitor activity<br />
**has_input UniProtKB:P29350 (PTPN6)<br />
* MF: GO:0097677 STAT family protein binding<br />
**has_input UniProtKB:P40763 (STAT3)<br />
<br />
BP terms to describe regulation of pathway and involvement in processes:<br />
* BP: GO:0046427 positive regulation of receptor signaling pathway via JAK-STAT<br />
* BP: GO0097028 dendritic cell differentiation<br />
<br />
<br />
[[Category:Annotation Guidelines]]</div>Hla28https://wiki.geneontology.org/index.php?title=LncRNA_GO_annotation_manual&diff=86638LncRNA GO annotation manual2024-03-06T21:59:53Z<p>Hla28: /* miRNA inhibitor activity */</p>
<hr />
<div>LncRNAs have multiple and varied activities (see [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]] which describes 13 roles of lncRNAs), these guidelines are suggestions for the curation of some of these lncRNAs. These were discussed [https://github.com/geneontology/go-ontology/issues/23028 here].<br />
<br />
===Decision tree to assist with curation of lncRNA:miRNA interactions===<br />
<br />
These guidelines are for the curation of lncRNAs that bind to miRNA and prevent miRNA activity. These lncRNAs are often described as sponge lncRNAs.<br />
<br />
Link to LncRNA_Decision_Tree pdf[[https://wiki.geneontology.org/images/e/e4/LncRNA_Decision_Tree.pdf]]<br />
<br />
[[File:LncRNA Decision Tree.jpg|960x540px]]<br />
<br />
'''Decision Tree for the GO terms and annotation extensions used for capturing targets of lncRNAs.''' The types of evidence in the blue boxes are described further in the text. Information about the cell or tissue that the interaction occurs in can be captured for example in the annotation extension field using: occurs_in (insert cell ontology ID and/or UBERON ID based on cell and/or tissue type respectively). This information can be included when inhibition of the lncRNA leads to an increase in the endogenous miRNA (or decrease in the miRNA target protein level). Slightly weaker evidence to support inclusion of the cell or tissue information would be evidence that the lncRNA is expressed in these cells/this tissue AND that the authors are confident that the lncRNA target is also being regulated in these cells/this tissue. For example, when the addition of the lncRNA leads to a decrease in the endogenous miRNA or increase in the endogenous protein level.<br />
<br />
'''Note:''' to be able to indicate any target in a GO annotation, the prediction evidence does not need to be in the paper you are annotating, it could be from another paper or a prediction database. When looking at predictions or validations in a prediction database, it is recommended to check the references cited for the target as they may serve as a good source of experimental annotation. Additionally, it has been found that some of the cited papers do not support the validation of the targets. Annotations to “miRNA inhibitor activity via base pairing” (GO:0140869) should ONLY be made from the paper containing the experimental evidence, however it is acceptable to indicate in the annotation extension of a “gene silencing by miRNA” annotation that the target of gene silencing is direct (by using ''has_input'') if the evidence for binding is in another paper.<br />
<br />
===Random inactivation of X chromosome===<br />
<br />
Figure 2b [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: Xist modulates inactive X chromosome (Xi) architecture during X chromosome inactivation (XCI) by recruiting Xi to associate with the lamin B receptor (LBR) at the nuclear lamina to silence transcription.<br />
<br />
LncRNA (Xist) Annotations:<br />
* MF: GO:0140463 chromatin-protein adaptor activity + appropriate information etc (eg part_of GO:0060820 inactivation of X chromosome by heterochromatin formation)<br />
* BF: GO:0060816 random inactivation of X chromosome<br />
<br />
=== DNA-DNA tethering activity ===<br />
<br />
Figure 2c [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: Firre transcripts localize to their transcription site and five additional autosomal chromosomal loci in trans to affect interactions between distant genomic regions.<br />
<br />
LncRNA (Firre) annotations:<br />
* MF: GO:0106260 DNA-DNA tethering activity + appropriate information etc (eg part_of GO:0006325 chromatin organization)<br />
* BP: GO:0006325 chromatin organization<br />
<br />
=== Promoter-enhancer loop anchoring activity ===<br />
<br />
Figure 2d [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: CCAT1-L accumulates in cis to modulate chromatin loops between enhancers and the promoter of MYC.<br />
<br />
LncRNA (CCAT1-L) annotations:<br />
* MF: GO:0140585 promoter-enhancer loop anchoring activity + appropriate information etc (eg part_of GO:0140588 chromatin looping)<br />
* BP: GO:0140588 chromatin looping<br />
<br />
=== Regulation of chromatin accessibility ===<br />
<br />
Figure 2e [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: lncRNAs regulate chromatin accessibility. Left, Xist recruits HDAC1-associated repressor protein (SHARP), silencing the mediator for retinoid and thyroid hormone receptor (SMART) and HDAC3 to silence Xi. Right, Mhrt prevents SWI/SNF binding to corresponding DNA loci.<br />
<br />
LncRNA (Xist) annotations:<br />
* MF: GO:0030674 protein-macromolecule adaptor activity + appropriate information (eg part_of GO:0006338 chromatin remodeling)<br />
* BP: GO:0006338 chromatin remodeling<br />
<br />
LncRNA (Mhrt) annotations based on [[https://pubmed.ncbi.nlm.nih.gov/25119045/ PMID:25119045]]:<br />
* MF: GO:0140311 protein sequestering activity + appropriate information etc (eg has_inputs Brg1/Smarca4, Q3TKT4), part_of GO:0006338 chromatin remodeling)<br />
* BP: GO:0006338 chromatin remodeling<br />
<br />
=== Triplex-Mediated Changes in Chromatin Structure ===<br />
<br />
Figure 2f, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: Khps1 enhances Pol II transcription by forming an R-loop that anchors Khps1-interacting p300/CBP to the SPHK1 promoter.<br />
<br />
LncRNA (Khps1) annotations based on [[https://pubmed.ncbi.nlm.nih.gov/26590717/ PMID: 26590717]]:<br />
<br />
* MF: GO:0030674 protein-macromolecule adaptor activity or GO:0001010 RNA polymerase II sequence-specific DNA-binding transcription factor recruiting activity + appropriate information etc (eg part_of GO:0045944 positive regulation of transcription by RNA polymerase II)<br />
* MF: GO:1990837 sequence-specific double-stranded DNA binding + appropriate information etc (eg part_of GO:0006325 chromatin organization)<br />
* BP: GO:0006325 chromatin organization<br />
* BP: GO:0045944 positive regulation of transcription by RNA polymerase II<br />
<br />
=== RNA polymerase inhibitor activity ===<br />
<br />
Figure 2g, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]:lncRNAs interfere with Pol II transcription machineries both at the initiation (left) and elongation (right) stages.<br />
<br />
LncRNA annotations:<br />
* MF: GO:0140870 RNA polymerase inhibitor activity<br />
* BP:GO:0000122 negative regulation of transcription by RNA polymerase II<br />
<br />
=== repressor of RNA polymerase inhibitor activity ===<br />
<br />
Figure 2h, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: SLERT promotes Pol I transcription by binding DDX21 to alter its conformation, thereby releasing its inhibitory effect on Pol I.<br />
<br />
LncRNA (SLERT) annotations:<br />
* MF: GO:0140871 repressor of RNA polymerase inhibitor activity + appropriate information (eg has_input DDX21)<br />
* BP: GO:0045943 positive regulation of transcription by RNA polymerase I<br />
<br />
=== molecular condensate scaffold activity ===<br />
<br />
Figure 2i, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: NEAT1 is an architectural lncRNA that nucleates paraspeckles. Upon cellular stress, altered NEAT1 transcription and processing lead to changes of paraspeckles. PSP, paraspeckle proteins.<br />
<br />
LncRNA (NEAT1) annotations:<br />
* MF: GO:0140693 molecular condensate scaffold activity + additional information (eg part_of GO:0006325 chromatin organization or GO:0006996 organelle organization)<br />
* BP: GO:0030575 nuclear body organization<br />
<br />
=== miRNA inhibitor activity ===<br />
<br />
See decision tree above <br />
Figure 2k, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]:Cyrano, harbouring miR-7 binding site and mediates its destruction by target-RNA-directed miRNA degradation.<br />
<br />
<br />
LncRNA Cyrano annotations e.g. mouse, URS000075A502_10090, URS000075B8A8_10090 [[https://pubmed.ncbi.nlm.nih.gov/29887379/ PMID:29887379]]. A Network of Noncoding Regulatory RNAs Acts in the Mammalian Brain. (2018)<br />
* MF GO:0140869 miRNA inhibitor activity via base-pairing<br />
** has_input URS0000591950_10090 (miR-7b-5p)& URS000075DE8D_10090 (miR-7a-5p) <br />
* BP: GO:0000512 lncRNA-mediated post-transcriptional gene silencing<br />
* BP: GO:0140958 target-directed miRNA degradation<br />
<br />
Note that the level of Cyrano does not change but the level of target miR-7 is down-regulated dramatically, as the lncRNA is not destroyed in the process. If the lncRNA decreases with the miRNA, then it is not target-directed miRNA degradation, but can be annotated with another more appropriate term such as GO:0010587 miRNA catabolic process.<br />
<br />
=== mRNA degradation ===<br />
<br />
Figure 2l, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: lncRNAs modulate mRNA stability by associating with proteins involved in mRNA degradation. Left, double-stranded RNAs formed by Alu-containing lncRNAs with mRNA 3′ UTRs recruit STAU1 to induce STAU1-mediated mRNA decay (SMD). Right, NORAD stabilizes PUMILIO 1/2 (PUM1/2)-targeted mRNAs via sequestering PUM1/2 from mRNAs.<br />
<br />
LncRNA (NORAD) annotations:<br />
* MF: GO:1903231 mRNA base-pairing translational repressor activity + additional information (eg part_of GO:0000512 lncRNA-mediated post-transcriptional gene silencing)<br />
* BP: GO:0000512 lncRNA-mediated post-transcriptional gene silencing<br />
<br />
=== mRNA translation repression ===<br />
<br />
Figure 2m, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: lncRNAs regulate translation. Association of lincRNA-p21 (linc-p21) with HuR favours the recruitment of let-7/Ago2, leading to its destabilization. In the absence of HuR, lincRNA-p21 identifies mRNA targets to repress their translation by recruiting the translation repressor Rck129. RISC, RNA-induced silencing complex.<br />
<br />
LncRNA annotations:<br />
* MF: GO:1903231 mRNA base-pairing translational repressor activity + additional information (eg part_of GO:0000512 lncRNA-mediated post-transcriptional gene silencing)<br />
* BP: GO:0000512 lncRNA-mediated post-transcriptional gene silencing<br />
<br />
=== regulation of post-translational modifications ===<br />
<br />
Figure 2n, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: lncRNAs modulate post-translational modifications. Lnc-DC directly interacts with STAT3 to prevent its dephosphorylation by SHP1 (PTPN6).<br />
(From PMID:31857450: Phosphorylated STAT3 translocates in to the nucleus and activates transcription involved in dendritic cell differentiation)<br />
<br />
LncRNA annotations URS00007B42BD_9606 (GenBank:KJ020271) and URS00007B3652_9606 (GenBank:KJ020272) from PMID:31857450 'The STAT3-binding long noncoding RNA lnc-DC controls human dendritic cell differentiation'<br />
* MF: GO:0019212 phosphatase inhibitor activity<br />
**has_input UniProtKB:P29350 (PTPN6)<br />
* MF: GO:0097677 STAT family protein binding<br />
**has_input UniProtKB:P40763 (STAT3)<br />
<br />
BP terms to describe regulation of pathway and involvement in processes:<br />
* BP: GO:0046427 positive regulation of receptor signaling pathway via JAK-STAT<br />
* BP: GO0097028 dendritic cell differentiation<br />
<br />
<br />
[[Category:Annotation Guidelines]]</div>Hla28https://wiki.geneontology.org/index.php?title=LncRNA_GO_annotation_manual&diff=86637LncRNA GO annotation manual2024-03-06T21:54:38Z<p>Hla28: /* miRNA inhibitor activity */</p>
<hr />
<div>LncRNAs have multiple and varied activities (see [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]] which describes 13 roles of lncRNAs), these guidelines are suggestions for the curation of some of these lncRNAs. These were discussed [https://github.com/geneontology/go-ontology/issues/23028 here].<br />
<br />
===Decision tree to assist with curation of lncRNA:miRNA interactions===<br />
<br />
These guidelines are for the curation of lncRNAs that bind to miRNA and prevent miRNA activity. These lncRNAs are often described as sponge lncRNAs.<br />
<br />
Link to LncRNA_Decision_Tree pdf[[https://wiki.geneontology.org/images/e/e4/LncRNA_Decision_Tree.pdf]]<br />
<br />
[[File:LncRNA Decision Tree.jpg|960x540px]]<br />
<br />
'''Decision Tree for the GO terms and annotation extensions used for capturing targets of lncRNAs.''' The types of evidence in the blue boxes are described further in the text. Information about the cell or tissue that the interaction occurs in can be captured for example in the annotation extension field using: occurs_in (insert cell ontology ID and/or UBERON ID based on cell and/or tissue type respectively). This information can be included when inhibition of the lncRNA leads to an increase in the endogenous miRNA (or decrease in the miRNA target protein level). Slightly weaker evidence to support inclusion of the cell or tissue information would be evidence that the lncRNA is expressed in these cells/this tissue AND that the authors are confident that the lncRNA target is also being regulated in these cells/this tissue. For example, when the addition of the lncRNA leads to a decrease in the endogenous miRNA or increase in the endogenous protein level.<br />
<br />
'''Note:''' to be able to indicate any target in a GO annotation, the prediction evidence does not need to be in the paper you are annotating, it could be from another paper or a prediction database. When looking at predictions or validations in a prediction database, it is recommended to check the references cited for the target as they may serve as a good source of experimental annotation. Additionally, it has been found that some of the cited papers do not support the validation of the targets. Annotations to “miRNA inhibitor activity via base pairing” (GO:0140869) should ONLY be made from the paper containing the experimental evidence, however it is acceptable to indicate in the annotation extension of a “gene silencing by miRNA” annotation that the target of gene silencing is direct (by using ''has_input'') if the evidence for binding is in another paper.<br />
<br />
===Random inactivation of X chromosome===<br />
<br />
Figure 2b [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: Xist modulates inactive X chromosome (Xi) architecture during X chromosome inactivation (XCI) by recruiting Xi to associate with the lamin B receptor (LBR) at the nuclear lamina to silence transcription.<br />
<br />
LncRNA (Xist) Annotations:<br />
* MF: GO:0140463 chromatin-protein adaptor activity + appropriate information etc (eg part_of GO:0060820 inactivation of X chromosome by heterochromatin formation)<br />
* BF: GO:0060816 random inactivation of X chromosome<br />
<br />
=== DNA-DNA tethering activity ===<br />
<br />
Figure 2c [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: Firre transcripts localize to their transcription site and five additional autosomal chromosomal loci in trans to affect interactions between distant genomic regions.<br />
<br />
LncRNA (Firre) annotations:<br />
* MF: GO:0106260 DNA-DNA tethering activity + appropriate information etc (eg part_of GO:0006325 chromatin organization)<br />
* BP: GO:0006325 chromatin organization<br />
<br />
=== Promoter-enhancer loop anchoring activity ===<br />
<br />
Figure 2d [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: CCAT1-L accumulates in cis to modulate chromatin loops between enhancers and the promoter of MYC.<br />
<br />
LncRNA (CCAT1-L) annotations:<br />
* MF: GO:0140585 promoter-enhancer loop anchoring activity + appropriate information etc (eg part_of GO:0140588 chromatin looping)<br />
* BP: GO:0140588 chromatin looping<br />
<br />
=== Regulation of chromatin accessibility ===<br />
<br />
Figure 2e [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: lncRNAs regulate chromatin accessibility. Left, Xist recruits HDAC1-associated repressor protein (SHARP), silencing the mediator for retinoid and thyroid hormone receptor (SMART) and HDAC3 to silence Xi. Right, Mhrt prevents SWI/SNF binding to corresponding DNA loci.<br />
<br />
LncRNA (Xist) annotations:<br />
* MF: GO:0030674 protein-macromolecule adaptor activity + appropriate information (eg part_of GO:0006338 chromatin remodeling)<br />
* BP: GO:0006338 chromatin remodeling<br />
<br />
LncRNA (Mhrt) annotations based on [[https://pubmed.ncbi.nlm.nih.gov/25119045/ PMID:25119045]]:<br />
* MF: GO:0140311 protein sequestering activity + appropriate information etc (eg has_inputs Brg1/Smarca4, Q3TKT4), part_of GO:0006338 chromatin remodeling)<br />
* BP: GO:0006338 chromatin remodeling<br />
<br />
=== Triplex-Mediated Changes in Chromatin Structure ===<br />
<br />
Figure 2f, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: Khps1 enhances Pol II transcription by forming an R-loop that anchors Khps1-interacting p300/CBP to the SPHK1 promoter.<br />
<br />
LncRNA (Khps1) annotations based on [[https://pubmed.ncbi.nlm.nih.gov/26590717/ PMID: 26590717]]:<br />
<br />
* MF: GO:0030674 protein-macromolecule adaptor activity or GO:0001010 RNA polymerase II sequence-specific DNA-binding transcription factor recruiting activity + appropriate information etc (eg part_of GO:0045944 positive regulation of transcription by RNA polymerase II)<br />
* MF: GO:1990837 sequence-specific double-stranded DNA binding + appropriate information etc (eg part_of GO:0006325 chromatin organization)<br />
* BP: GO:0006325 chromatin organization<br />
* BP: GO:0045944 positive regulation of transcription by RNA polymerase II<br />
<br />
=== RNA polymerase inhibitor activity ===<br />
<br />
Figure 2g, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]:lncRNAs interfere with Pol II transcription machineries both at the initiation (left) and elongation (right) stages.<br />
<br />
LncRNA annotations:<br />
* MF: GO:0140870 RNA polymerase inhibitor activity<br />
* BP:GO:0000122 negative regulation of transcription by RNA polymerase II<br />
<br />
=== repressor of RNA polymerase inhibitor activity ===<br />
<br />
Figure 2h, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: SLERT promotes Pol I transcription by binding DDX21 to alter its conformation, thereby releasing its inhibitory effect on Pol I.<br />
<br />
LncRNA (SLERT) annotations:<br />
* MF: GO:0140871 repressor of RNA polymerase inhibitor activity + appropriate information (eg has_input DDX21)<br />
* BP: GO:0045943 positive regulation of transcription by RNA polymerase I<br />
<br />
=== molecular condensate scaffold activity ===<br />
<br />
Figure 2i, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: NEAT1 is an architectural lncRNA that nucleates paraspeckles. Upon cellular stress, altered NEAT1 transcription and processing lead to changes of paraspeckles. PSP, paraspeckle proteins.<br />
<br />
LncRNA (NEAT1) annotations:<br />
* MF: GO:0140693 molecular condensate scaffold activity + additional information (eg part_of GO:0006325 chromatin organization or GO:0006996 organelle organization)<br />
* BP: GO:0030575 nuclear body organization<br />
<br />
=== miRNA inhibitor activity ===<br />
<br />
See decision tree above <br />
Figure 2k, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]:Cyrano, harbouring miR-7 binding site and mediates its destruction by target-RNA-directed miRNA degradation.<br />
<br />
LncRNA Cyrano annotations e.g. mouse, URS000075A502_10090, URS000075B8A8_10090 [[https://pubmed.ncbi.nlm.nih.gov/29887379/ PMID:29887379]]. A Network of Noncoding Regulatory RNAs Acts in the Mammalian Brain. (2018)<br />
* MF GO:0140869 miRNA inhibitor activity via base-pairing<br />
** has_input URS0000591950_10090 (miR-7b-5p)& URS000075DE8D_10090 (miR-7a-5p) <br />
* BP: GO:0000512 lncRNA-mediated post-transcriptional gene silencing<br />
* BP: GO:0140958 target-directed miRNA degradation<br />
<br />
=== mRNA degradation ===<br />
<br />
Figure 2l, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: lncRNAs modulate mRNA stability by associating with proteins involved in mRNA degradation. Left, double-stranded RNAs formed by Alu-containing lncRNAs with mRNA 3′ UTRs recruit STAU1 to induce STAU1-mediated mRNA decay (SMD). Right, NORAD stabilizes PUMILIO 1/2 (PUM1/2)-targeted mRNAs via sequestering PUM1/2 from mRNAs.<br />
<br />
LncRNA (NORAD) annotations:<br />
* MF: GO:1903231 mRNA base-pairing translational repressor activity + additional information (eg part_of GO:0000512 lncRNA-mediated post-transcriptional gene silencing)<br />
* BP: GO:0000512 lncRNA-mediated post-transcriptional gene silencing<br />
<br />
=== mRNA translation repression ===<br />
<br />
Figure 2m, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: lncRNAs regulate translation. Association of lincRNA-p21 (linc-p21) with HuR favours the recruitment of let-7/Ago2, leading to its destabilization. In the absence of HuR, lincRNA-p21 identifies mRNA targets to repress their translation by recruiting the translation repressor Rck129. RISC, RNA-induced silencing complex.<br />
<br />
LncRNA annotations:<br />
* MF: GO:1903231 mRNA base-pairing translational repressor activity + additional information (eg part_of GO:0000512 lncRNA-mediated post-transcriptional gene silencing)<br />
* BP: GO:0000512 lncRNA-mediated post-transcriptional gene silencing<br />
<br />
=== regulation of post-translational modifications ===<br />
<br />
Figure 2n, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: lncRNAs modulate post-translational modifications. Lnc-DC directly interacts with STAT3 to prevent its dephosphorylation by SHP1 (PTPN6).<br />
(From PMID:31857450: Phosphorylated STAT3 translocates in to the nucleus and activates transcription involved in dendritic cell differentiation)<br />
<br />
LncRNA annotations URS00007B42BD_9606 (GenBank:KJ020271) and URS00007B3652_9606 (GenBank:KJ020272) from PMID:31857450 'The STAT3-binding long noncoding RNA lnc-DC controls human dendritic cell differentiation'<br />
* MF: GO:0019212 phosphatase inhibitor activity<br />
**has_input UniProtKB:P29350 (PTPN6)<br />
* MF: GO:0097677 STAT family protein binding<br />
**has_input UniProtKB:P40763 (STAT3)<br />
<br />
BP terms to describe regulation of pathway and involvement in processes:<br />
* BP: GO:0046427 positive regulation of receptor signaling pathway via JAK-STAT<br />
* BP: GO0097028 dendritic cell differentiation<br />
<br />
<br />
[[Category:Annotation Guidelines]]</div>Hla28https://wiki.geneontology.org/index.php?title=LncRNA_GO_annotation_manual&diff=86636LncRNA GO annotation manual2024-03-06T21:49:33Z<p>Hla28: /* miRNA inhibitor activity */</p>
<hr />
<div>LncRNAs have multiple and varied activities (see [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]] which describes 13 roles of lncRNAs), these guidelines are suggestions for the curation of some of these lncRNAs. These were discussed [https://github.com/geneontology/go-ontology/issues/23028 here].<br />
<br />
===Decision tree to assist with curation of lncRNA:miRNA interactions===<br />
<br />
These guidelines are for the curation of lncRNAs that bind to miRNA and prevent miRNA activity. These lncRNAs are often described as sponge lncRNAs.<br />
<br />
Link to LncRNA_Decision_Tree pdf[[https://wiki.geneontology.org/images/e/e4/LncRNA_Decision_Tree.pdf]]<br />
<br />
[[File:LncRNA Decision Tree.jpg|960x540px]]<br />
<br />
'''Decision Tree for the GO terms and annotation extensions used for capturing targets of lncRNAs.''' The types of evidence in the blue boxes are described further in the text. Information about the cell or tissue that the interaction occurs in can be captured for example in the annotation extension field using: occurs_in (insert cell ontology ID and/or UBERON ID based on cell and/or tissue type respectively). This information can be included when inhibition of the lncRNA leads to an increase in the endogenous miRNA (or decrease in the miRNA target protein level). Slightly weaker evidence to support inclusion of the cell or tissue information would be evidence that the lncRNA is expressed in these cells/this tissue AND that the authors are confident that the lncRNA target is also being regulated in these cells/this tissue. For example, when the addition of the lncRNA leads to a decrease in the endogenous miRNA or increase in the endogenous protein level.<br />
<br />
'''Note:''' to be able to indicate any target in a GO annotation, the prediction evidence does not need to be in the paper you are annotating, it could be from another paper or a prediction database. When looking at predictions or validations in a prediction database, it is recommended to check the references cited for the target as they may serve as a good source of experimental annotation. Additionally, it has been found that some of the cited papers do not support the validation of the targets. Annotations to “miRNA inhibitor activity via base pairing” (GO:0140869) should ONLY be made from the paper containing the experimental evidence, however it is acceptable to indicate in the annotation extension of a “gene silencing by miRNA” annotation that the target of gene silencing is direct (by using ''has_input'') if the evidence for binding is in another paper.<br />
<br />
===Random inactivation of X chromosome===<br />
<br />
Figure 2b [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: Xist modulates inactive X chromosome (Xi) architecture during X chromosome inactivation (XCI) by recruiting Xi to associate with the lamin B receptor (LBR) at the nuclear lamina to silence transcription.<br />
<br />
LncRNA (Xist) Annotations:<br />
* MF: GO:0140463 chromatin-protein adaptor activity + appropriate information etc (eg part_of GO:0060820 inactivation of X chromosome by heterochromatin formation)<br />
* BF: GO:0060816 random inactivation of X chromosome<br />
<br />
=== DNA-DNA tethering activity ===<br />
<br />
Figure 2c [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: Firre transcripts localize to their transcription site and five additional autosomal chromosomal loci in trans to affect interactions between distant genomic regions.<br />
<br />
LncRNA (Firre) annotations:<br />
* MF: GO:0106260 DNA-DNA tethering activity + appropriate information etc (eg part_of GO:0006325 chromatin organization)<br />
* BP: GO:0006325 chromatin organization<br />
<br />
=== Promoter-enhancer loop anchoring activity ===<br />
<br />
Figure 2d [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: CCAT1-L accumulates in cis to modulate chromatin loops between enhancers and the promoter of MYC.<br />
<br />
LncRNA (CCAT1-L) annotations:<br />
* MF: GO:0140585 promoter-enhancer loop anchoring activity + appropriate information etc (eg part_of GO:0140588 chromatin looping)<br />
* BP: GO:0140588 chromatin looping<br />
<br />
=== Regulation of chromatin accessibility ===<br />
<br />
Figure 2e [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: lncRNAs regulate chromatin accessibility. Left, Xist recruits HDAC1-associated repressor protein (SHARP), silencing the mediator for retinoid and thyroid hormone receptor (SMART) and HDAC3 to silence Xi. Right, Mhrt prevents SWI/SNF binding to corresponding DNA loci.<br />
<br />
LncRNA (Xist) annotations:<br />
* MF: GO:0030674 protein-macromolecule adaptor activity + appropriate information (eg part_of GO:0006338 chromatin remodeling)<br />
* BP: GO:0006338 chromatin remodeling<br />
<br />
LncRNA (Mhrt) annotations based on [[https://pubmed.ncbi.nlm.nih.gov/25119045/ PMID:25119045]]:<br />
* MF: GO:0140311 protein sequestering activity + appropriate information etc (eg has_inputs Brg1/Smarca4, Q3TKT4), part_of GO:0006338 chromatin remodeling)<br />
* BP: GO:0006338 chromatin remodeling<br />
<br />
=== Triplex-Mediated Changes in Chromatin Structure ===<br />
<br />
Figure 2f, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: Khps1 enhances Pol II transcription by forming an R-loop that anchors Khps1-interacting p300/CBP to the SPHK1 promoter.<br />
<br />
LncRNA (Khps1) annotations based on [[https://pubmed.ncbi.nlm.nih.gov/26590717/ PMID: 26590717]]:<br />
<br />
* MF: GO:0030674 protein-macromolecule adaptor activity or GO:0001010 RNA polymerase II sequence-specific DNA-binding transcription factor recruiting activity + appropriate information etc (eg part_of GO:0045944 positive regulation of transcription by RNA polymerase II)<br />
* MF: GO:1990837 sequence-specific double-stranded DNA binding + appropriate information etc (eg part_of GO:0006325 chromatin organization)<br />
* BP: GO:0006325 chromatin organization<br />
* BP: GO:0045944 positive regulation of transcription by RNA polymerase II<br />
<br />
=== RNA polymerase inhibitor activity ===<br />
<br />
Figure 2g, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]:lncRNAs interfere with Pol II transcription machineries both at the initiation (left) and elongation (right) stages.<br />
<br />
LncRNA annotations:<br />
* MF: GO:0140870 RNA polymerase inhibitor activity<br />
* BP:GO:0000122 negative regulation of transcription by RNA polymerase II<br />
<br />
=== repressor of RNA polymerase inhibitor activity ===<br />
<br />
Figure 2h, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: SLERT promotes Pol I transcription by binding DDX21 to alter its conformation, thereby releasing its inhibitory effect on Pol I.<br />
<br />
LncRNA (SLERT) annotations:<br />
* MF: GO:0140871 repressor of RNA polymerase inhibitor activity + appropriate information (eg has_input DDX21)<br />
* BP: GO:0045943 positive regulation of transcription by RNA polymerase I<br />
<br />
=== molecular condensate scaffold activity ===<br />
<br />
Figure 2i, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: NEAT1 is an architectural lncRNA that nucleates paraspeckles. Upon cellular stress, altered NEAT1 transcription and processing lead to changes of paraspeckles. PSP, paraspeckle proteins.<br />
<br />
LncRNA (NEAT1) annotations:<br />
* MF: GO:0140693 molecular condensate scaffold activity + additional information (eg part_of GO:0006325 chromatin organization or GO:0006996 organelle organization)<br />
* BP: GO:0030575 nuclear body organization<br />
<br />
=== miRNA inhibitor activity ===<br />
<br />
See decision tree above <br />
Figure 2k, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]:Cyrano, harbouring miR-7 binding site and mediates its destruction by target-RNA-directed miRNA degradation.<br />
<br />
LncRNA Cyrano annotations e.g. mouse, URS000075A502_10090, URS000075B8A8_10090 [[https://pubmed.ncbi.nlm.nih.gov/29887379/ PMID:29887379]]. A Network of Noncoding Regulatory RNAs Acts in the Mammalian Brain. (2018)<br />
* MF GO:0140869 miRNA inhibitor activity via base-pairing + additional information (eg has_input miR-7 RNAcentral ID, part_of GO:0000512 lncRNA-mediated post-transcriptional gene silencing)<br />
* BP: GO:0000512 lncRNA-mediated post-transcriptional gene silencing<br />
* BP: GO:0140958 target-directed miRNA degradation<br />
<br />
=== mRNA degradation ===<br />
<br />
Figure 2l, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: lncRNAs modulate mRNA stability by associating with proteins involved in mRNA degradation. Left, double-stranded RNAs formed by Alu-containing lncRNAs with mRNA 3′ UTRs recruit STAU1 to induce STAU1-mediated mRNA decay (SMD). Right, NORAD stabilizes PUMILIO 1/2 (PUM1/2)-targeted mRNAs via sequestering PUM1/2 from mRNAs.<br />
<br />
LncRNA (NORAD) annotations:<br />
* MF: GO:1903231 mRNA base-pairing translational repressor activity + additional information (eg part_of GO:0000512 lncRNA-mediated post-transcriptional gene silencing)<br />
* BP: GO:0000512 lncRNA-mediated post-transcriptional gene silencing<br />
<br />
=== mRNA translation repression ===<br />
<br />
Figure 2m, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: lncRNAs regulate translation. Association of lincRNA-p21 (linc-p21) with HuR favours the recruitment of let-7/Ago2, leading to its destabilization. In the absence of HuR, lincRNA-p21 identifies mRNA targets to repress their translation by recruiting the translation repressor Rck129. RISC, RNA-induced silencing complex.<br />
<br />
LncRNA annotations:<br />
* MF: GO:1903231 mRNA base-pairing translational repressor activity + additional information (eg part_of GO:0000512 lncRNA-mediated post-transcriptional gene silencing)<br />
* BP: GO:0000512 lncRNA-mediated post-transcriptional gene silencing<br />
<br />
=== regulation of post-translational modifications ===<br />
<br />
Figure 2n, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: lncRNAs modulate post-translational modifications. Lnc-DC directly interacts with STAT3 to prevent its dephosphorylation by SHP1 (PTPN6).<br />
(From PMID:31857450: Phosphorylated STAT3 translocates in to the nucleus and activates transcription involved in dendritic cell differentiation)<br />
<br />
LncRNA annotations URS00007B42BD_9606 (GenBank:KJ020271) and URS00007B3652_9606 (GenBank:KJ020272) from PMID:31857450 'The STAT3-binding long noncoding RNA lnc-DC controls human dendritic cell differentiation'<br />
* MF: GO:0019212 phosphatase inhibitor activity<br />
**has_input UniProtKB:P29350 (PTPN6)<br />
* MF: GO:0097677 STAT family protein binding<br />
**has_input UniProtKB:P40763 (STAT3)<br />
<br />
BP terms to describe regulation of pathway and involvement in processes:<br />
* BP: GO:0046427 positive regulation of receptor signaling pathway via JAK-STAT<br />
* BP: GO0097028 dendritic cell differentiation<br />
<br />
<br />
[[Category:Annotation Guidelines]]</div>Hla28https://wiki.geneontology.org/index.php?title=LncRNA_GO_annotation_manual&diff=86635LncRNA GO annotation manual2024-03-06T21:48:41Z<p>Hla28: /* miRNA inhibitor activity */</p>
<hr />
<div>LncRNAs have multiple and varied activities (see [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]] which describes 13 roles of lncRNAs), these guidelines are suggestions for the curation of some of these lncRNAs. These were discussed [https://github.com/geneontology/go-ontology/issues/23028 here].<br />
<br />
===Decision tree to assist with curation of lncRNA:miRNA interactions===<br />
<br />
These guidelines are for the curation of lncRNAs that bind to miRNA and prevent miRNA activity. These lncRNAs are often described as sponge lncRNAs.<br />
<br />
Link to LncRNA_Decision_Tree pdf[[https://wiki.geneontology.org/images/e/e4/LncRNA_Decision_Tree.pdf]]<br />
<br />
[[File:LncRNA Decision Tree.jpg|960x540px]]<br />
<br />
'''Decision Tree for the GO terms and annotation extensions used for capturing targets of lncRNAs.''' The types of evidence in the blue boxes are described further in the text. Information about the cell or tissue that the interaction occurs in can be captured for example in the annotation extension field using: occurs_in (insert cell ontology ID and/or UBERON ID based on cell and/or tissue type respectively). This information can be included when inhibition of the lncRNA leads to an increase in the endogenous miRNA (or decrease in the miRNA target protein level). Slightly weaker evidence to support inclusion of the cell or tissue information would be evidence that the lncRNA is expressed in these cells/this tissue AND that the authors are confident that the lncRNA target is also being regulated in these cells/this tissue. For example, when the addition of the lncRNA leads to a decrease in the endogenous miRNA or increase in the endogenous protein level.<br />
<br />
'''Note:''' to be able to indicate any target in a GO annotation, the prediction evidence does not need to be in the paper you are annotating, it could be from another paper or a prediction database. When looking at predictions or validations in a prediction database, it is recommended to check the references cited for the target as they may serve as a good source of experimental annotation. Additionally, it has been found that some of the cited papers do not support the validation of the targets. Annotations to “miRNA inhibitor activity via base pairing” (GO:0140869) should ONLY be made from the paper containing the experimental evidence, however it is acceptable to indicate in the annotation extension of a “gene silencing by miRNA” annotation that the target of gene silencing is direct (by using ''has_input'') if the evidence for binding is in another paper.<br />
<br />
===Random inactivation of X chromosome===<br />
<br />
Figure 2b [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: Xist modulates inactive X chromosome (Xi) architecture during X chromosome inactivation (XCI) by recruiting Xi to associate with the lamin B receptor (LBR) at the nuclear lamina to silence transcription.<br />
<br />
LncRNA (Xist) Annotations:<br />
* MF: GO:0140463 chromatin-protein adaptor activity + appropriate information etc (eg part_of GO:0060820 inactivation of X chromosome by heterochromatin formation)<br />
* BF: GO:0060816 random inactivation of X chromosome<br />
<br />
=== DNA-DNA tethering activity ===<br />
<br />
Figure 2c [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: Firre transcripts localize to their transcription site and five additional autosomal chromosomal loci in trans to affect interactions between distant genomic regions.<br />
<br />
LncRNA (Firre) annotations:<br />
* MF: GO:0106260 DNA-DNA tethering activity + appropriate information etc (eg part_of GO:0006325 chromatin organization)<br />
* BP: GO:0006325 chromatin organization<br />
<br />
=== Promoter-enhancer loop anchoring activity ===<br />
<br />
Figure 2d [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: CCAT1-L accumulates in cis to modulate chromatin loops between enhancers and the promoter of MYC.<br />
<br />
LncRNA (CCAT1-L) annotations:<br />
* MF: GO:0140585 promoter-enhancer loop anchoring activity + appropriate information etc (eg part_of GO:0140588 chromatin looping)<br />
* BP: GO:0140588 chromatin looping<br />
<br />
=== Regulation of chromatin accessibility ===<br />
<br />
Figure 2e [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: lncRNAs regulate chromatin accessibility. Left, Xist recruits HDAC1-associated repressor protein (SHARP), silencing the mediator for retinoid and thyroid hormone receptor (SMART) and HDAC3 to silence Xi. Right, Mhrt prevents SWI/SNF binding to corresponding DNA loci.<br />
<br />
LncRNA (Xist) annotations:<br />
* MF: GO:0030674 protein-macromolecule adaptor activity + appropriate information (eg part_of GO:0006338 chromatin remodeling)<br />
* BP: GO:0006338 chromatin remodeling<br />
<br />
LncRNA (Mhrt) annotations based on [[https://pubmed.ncbi.nlm.nih.gov/25119045/ PMID:25119045]]:<br />
* MF: GO:0140311 protein sequestering activity + appropriate information etc (eg has_inputs Brg1/Smarca4, Q3TKT4), part_of GO:0006338 chromatin remodeling)<br />
* BP: GO:0006338 chromatin remodeling<br />
<br />
=== Triplex-Mediated Changes in Chromatin Structure ===<br />
<br />
Figure 2f, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: Khps1 enhances Pol II transcription by forming an R-loop that anchors Khps1-interacting p300/CBP to the SPHK1 promoter.<br />
<br />
LncRNA (Khps1) annotations based on [[https://pubmed.ncbi.nlm.nih.gov/26590717/ PMID: 26590717]]:<br />
<br />
* MF: GO:0030674 protein-macromolecule adaptor activity or GO:0001010 RNA polymerase II sequence-specific DNA-binding transcription factor recruiting activity + appropriate information etc (eg part_of GO:0045944 positive regulation of transcription by RNA polymerase II)<br />
* MF: GO:1990837 sequence-specific double-stranded DNA binding + appropriate information etc (eg part_of GO:0006325 chromatin organization)<br />
* BP: GO:0006325 chromatin organization<br />
* BP: GO:0045944 positive regulation of transcription by RNA polymerase II<br />
<br />
=== RNA polymerase inhibitor activity ===<br />
<br />
Figure 2g, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]:lncRNAs interfere with Pol II transcription machineries both at the initiation (left) and elongation (right) stages.<br />
<br />
LncRNA annotations:<br />
* MF: GO:0140870 RNA polymerase inhibitor activity<br />
* BP:GO:0000122 negative regulation of transcription by RNA polymerase II<br />
<br />
=== repressor of RNA polymerase inhibitor activity ===<br />
<br />
Figure 2h, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: SLERT promotes Pol I transcription by binding DDX21 to alter its conformation, thereby releasing its inhibitory effect on Pol I.<br />
<br />
LncRNA (SLERT) annotations:<br />
* MF: GO:0140871 repressor of RNA polymerase inhibitor activity + appropriate information (eg has_input DDX21)<br />
* BP: GO:0045943 positive regulation of transcription by RNA polymerase I<br />
<br />
=== molecular condensate scaffold activity ===<br />
<br />
Figure 2i, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: NEAT1 is an architectural lncRNA that nucleates paraspeckles. Upon cellular stress, altered NEAT1 transcription and processing lead to changes of paraspeckles. PSP, paraspeckle proteins.<br />
<br />
LncRNA (NEAT1) annotations:<br />
* MF: GO:0140693 molecular condensate scaffold activity + additional information (eg part_of GO:0006325 chromatin organization or GO:0006996 organelle organization)<br />
* BP: GO:0030575 nuclear body organization<br />
<br />
=== miRNA inhibitor activity ===<br />
<br />
See decision tree above <br />
Figure 2k, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]:Cyrano, harbouring miR-7 binding site and mediates its destruction by target-RNA-directed miRNA degradation.<br />
<br />
LncRNA Cyrano annotations e.g. mouse, URS000075A502_10090, URS000075B8A8_10090 PMID:29887379. A Network of Noncoding Regulatory RNAs Acts in the Mammalian Brain. (2018)<br />
* MF GO:0140869 miRNA inhibitor activity via base-pairing + additional information (eg has_input miR-7 RNAcentral ID, part_of GO:0000512 lncRNA-mediated post-transcriptional gene silencing)<br />
* BP: GO:0000512 lncRNA-mediated post-transcriptional gene silencing<br />
* BP: GO:0140958 target-directed miRNA degradation<br />
<br />
=== mRNA degradation ===<br />
<br />
Figure 2l, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: lncRNAs modulate mRNA stability by associating with proteins involved in mRNA degradation. Left, double-stranded RNAs formed by Alu-containing lncRNAs with mRNA 3′ UTRs recruit STAU1 to induce STAU1-mediated mRNA decay (SMD). Right, NORAD stabilizes PUMILIO 1/2 (PUM1/2)-targeted mRNAs via sequestering PUM1/2 from mRNAs.<br />
<br />
LncRNA (NORAD) annotations:<br />
* MF: GO:1903231 mRNA base-pairing translational repressor activity + additional information (eg part_of GO:0000512 lncRNA-mediated post-transcriptional gene silencing)<br />
* BP: GO:0000512 lncRNA-mediated post-transcriptional gene silencing<br />
<br />
=== mRNA translation repression ===<br />
<br />
Figure 2m, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: lncRNAs regulate translation. Association of lincRNA-p21 (linc-p21) with HuR favours the recruitment of let-7/Ago2, leading to its destabilization. In the absence of HuR, lincRNA-p21 identifies mRNA targets to repress their translation by recruiting the translation repressor Rck129. RISC, RNA-induced silencing complex.<br />
<br />
LncRNA annotations:<br />
* MF: GO:1903231 mRNA base-pairing translational repressor activity + additional information (eg part_of GO:0000512 lncRNA-mediated post-transcriptional gene silencing)<br />
* BP: GO:0000512 lncRNA-mediated post-transcriptional gene silencing<br />
<br />
=== regulation of post-translational modifications ===<br />
<br />
Figure 2n, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: lncRNAs modulate post-translational modifications. Lnc-DC directly interacts with STAT3 to prevent its dephosphorylation by SHP1 (PTPN6).<br />
(From PMID:31857450: Phosphorylated STAT3 translocates in to the nucleus and activates transcription involved in dendritic cell differentiation)<br />
<br />
LncRNA annotations URS00007B42BD_9606 (GenBank:KJ020271) and URS00007B3652_9606 (GenBank:KJ020272) from PMID:31857450 'The STAT3-binding long noncoding RNA lnc-DC controls human dendritic cell differentiation'<br />
* MF: GO:0019212 phosphatase inhibitor activity<br />
**has_input UniProtKB:P29350 (PTPN6)<br />
* MF: GO:0097677 STAT family protein binding<br />
**has_input UniProtKB:P40763 (STAT3)<br />
<br />
BP terms to describe regulation of pathway and involvement in processes:<br />
* BP: GO:0046427 positive regulation of receptor signaling pathway via JAK-STAT<br />
* BP: GO0097028 dendritic cell differentiation<br />
<br />
<br />
[[Category:Annotation Guidelines]]</div>Hla28https://wiki.geneontology.org/index.php?title=LncRNA_GO_annotation_manual&diff=86634LncRNA GO annotation manual2024-03-06T18:41:34Z<p>Hla28: /* miRNA inhibitor activity / sponge */</p>
<hr />
<div>LncRNAs have multiple and varied activities (see [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]] which describes 13 roles of lncRNAs), these guidelines are suggestions for the curation of some of these lncRNAs. These were discussed [https://github.com/geneontology/go-ontology/issues/23028 here].<br />
<br />
===Decision tree to assist with curation of lncRNA:miRNA interactions===<br />
<br />
These guidelines are for the curation of lncRNAs that bind to miRNA and prevent miRNA activity. These lncRNAs are often described as sponge lncRNAs.<br />
<br />
Link to LncRNA_Decision_Tree pdf[[https://wiki.geneontology.org/images/e/e4/LncRNA_Decision_Tree.pdf]]<br />
<br />
[[File:LncRNA Decision Tree.jpg|960x540px]]<br />
<br />
'''Decision Tree for the GO terms and annotation extensions used for capturing targets of lncRNAs.''' The types of evidence in the blue boxes are described further in the text. Information about the cell or tissue that the interaction occurs in can be captured for example in the annotation extension field using: occurs_in (insert cell ontology ID and/or UBERON ID based on cell and/or tissue type respectively). This information can be included when inhibition of the lncRNA leads to an increase in the endogenous miRNA (or decrease in the miRNA target protein level). Slightly weaker evidence to support inclusion of the cell or tissue information would be evidence that the lncRNA is expressed in these cells/this tissue AND that the authors are confident that the lncRNA target is also being regulated in these cells/this tissue. For example, when the addition of the lncRNA leads to a decrease in the endogenous miRNA or increase in the endogenous protein level.<br />
<br />
'''Note:''' to be able to indicate any target in a GO annotation, the prediction evidence does not need to be in the paper you are annotating, it could be from another paper or a prediction database. When looking at predictions or validations in a prediction database, it is recommended to check the references cited for the target as they may serve as a good source of experimental annotation. Additionally, it has been found that some of the cited papers do not support the validation of the targets. Annotations to “miRNA inhibitor activity via base pairing” (GO:0140869) should ONLY be made from the paper containing the experimental evidence, however it is acceptable to indicate in the annotation extension of a “gene silencing by miRNA” annotation that the target of gene silencing is direct (by using ''has_input'') if the evidence for binding is in another paper.<br />
<br />
===Random inactivation of X chromosome===<br />
<br />
Figure 2b [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: Xist modulates inactive X chromosome (Xi) architecture during X chromosome inactivation (XCI) by recruiting Xi to associate with the lamin B receptor (LBR) at the nuclear lamina to silence transcription.<br />
<br />
LncRNA (Xist) Annotations:<br />
* MF: GO:0140463 chromatin-protein adaptor activity + appropriate information etc (eg part_of GO:0060820 inactivation of X chromosome by heterochromatin formation)<br />
* BF: GO:0060816 random inactivation of X chromosome<br />
<br />
=== DNA-DNA tethering activity ===<br />
<br />
Figure 2c [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: Firre transcripts localize to their transcription site and five additional autosomal chromosomal loci in trans to affect interactions between distant genomic regions.<br />
<br />
LncRNA (Firre) annotations:<br />
* MF: GO:0106260 DNA-DNA tethering activity + appropriate information etc (eg part_of GO:0006325 chromatin organization)<br />
* BP: GO:0006325 chromatin organization<br />
<br />
=== Promoter-enhancer loop anchoring activity ===<br />
<br />
Figure 2d [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: CCAT1-L accumulates in cis to modulate chromatin loops between enhancers and the promoter of MYC.<br />
<br />
LncRNA (CCAT1-L) annotations:<br />
* MF: GO:0140585 promoter-enhancer loop anchoring activity + appropriate information etc (eg part_of GO:0140588 chromatin looping)<br />
* BP: GO:0140588 chromatin looping<br />
<br />
=== Regulation of chromatin accessibility ===<br />
<br />
Figure 2e [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: lncRNAs regulate chromatin accessibility. Left, Xist recruits HDAC1-associated repressor protein (SHARP), silencing the mediator for retinoid and thyroid hormone receptor (SMART) and HDAC3 to silence Xi. Right, Mhrt prevents SWI/SNF binding to corresponding DNA loci.<br />
<br />
LncRNA (Xist) annotations:<br />
* MF: GO:0030674 protein-macromolecule adaptor activity + appropriate information (eg part_of GO:0006338 chromatin remodeling)<br />
* BP: GO:0006338 chromatin remodeling<br />
<br />
LncRNA (Mhrt) annotations based on [[https://pubmed.ncbi.nlm.nih.gov/25119045/ PMID:25119045]]:<br />
* MF: GO:0140311 protein sequestering activity + appropriate information etc (eg has_inputs Brg1/Smarca4, Q3TKT4), part_of GO:0006338 chromatin remodeling)<br />
* BP: GO:0006338 chromatin remodeling<br />
<br />
=== Triplex-Mediated Changes in Chromatin Structure ===<br />
<br />
Figure 2f, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: Khps1 enhances Pol II transcription by forming an R-loop that anchors Khps1-interacting p300/CBP to the SPHK1 promoter.<br />
<br />
LncRNA (Khps1) annotations based on [[https://pubmed.ncbi.nlm.nih.gov/26590717/ PMID: 26590717]]:<br />
<br />
* MF: GO:0030674 protein-macromolecule adaptor activity or GO:0001010 RNA polymerase II sequence-specific DNA-binding transcription factor recruiting activity + appropriate information etc (eg part_of GO:0045944 positive regulation of transcription by RNA polymerase II)<br />
* MF: GO:1990837 sequence-specific double-stranded DNA binding + appropriate information etc (eg part_of GO:0006325 chromatin organization)<br />
* BP: GO:0006325 chromatin organization<br />
* BP: GO:0045944 positive regulation of transcription by RNA polymerase II<br />
<br />
=== RNA polymerase inhibitor activity ===<br />
<br />
Figure 2g, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]:lncRNAs interfere with Pol II transcription machineries both at the initiation (left) and elongation (right) stages.<br />
<br />
LncRNA annotations:<br />
* MF: GO:0140870 RNA polymerase inhibitor activity<br />
* BP:GO:0000122 negative regulation of transcription by RNA polymerase II<br />
<br />
=== repressor of RNA polymerase inhibitor activity ===<br />
<br />
Figure 2h, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: SLERT promotes Pol I transcription by binding DDX21 to alter its conformation, thereby releasing its inhibitory effect on Pol I.<br />
<br />
LncRNA (SLERT) annotations:<br />
* MF: GO:0140871 repressor of RNA polymerase inhibitor activity + appropriate information (eg has_input DDX21)<br />
* BP: GO:0045943 positive regulation of transcription by RNA polymerase I<br />
<br />
=== molecular condensate scaffold activity ===<br />
<br />
Figure 2i, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: NEAT1 is an architectural lncRNA that nucleates paraspeckles. Upon cellular stress, altered NEAT1 transcription and processing lead to changes of paraspeckles. PSP, paraspeckle proteins.<br />
<br />
LncRNA (NEAT1) annotations:<br />
* MF: GO:0140693 molecular condensate scaffold activity + additional information (eg part_of GO:0006325 chromatin organization or GO:0006996 organelle organization)<br />
* BP: GO:0030575 nuclear body organization<br />
<br />
=== miRNA inhibitor activity ===<br />
<br />
See decision tree above <br />
Figure 2k, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]:Cyrano, harbouring miR-7 binding site and mediates its destruction by target-RNA-directed miRNA degradation.<br />
<br />
LncRNA (Cyrano) annotations: <br />
* MF GO:0140869 miRNA inhibitor activity via base-pairing + additional information (eg has_input miR-7 RNAcentral ID, part_of GO:0000512 lncRNA-mediated post-transcriptional gene silencing)<br />
* BP: GO:0000512 lncRNA-mediated post-transcriptional gene silencing<br />
* BP: GO:0140958 target-directed miRNA degradation<br />
<br />
=== mRNA degradation ===<br />
<br />
Figure 2l, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: lncRNAs modulate mRNA stability by associating with proteins involved in mRNA degradation. Left, double-stranded RNAs formed by Alu-containing lncRNAs with mRNA 3′ UTRs recruit STAU1 to induce STAU1-mediated mRNA decay (SMD). Right, NORAD stabilizes PUMILIO 1/2 (PUM1/2)-targeted mRNAs via sequestering PUM1/2 from mRNAs.<br />
<br />
LncRNA (NORAD) annotations:<br />
* MF: GO:1903231 mRNA base-pairing translational repressor activity + additional information (eg part_of GO:0000512 lncRNA-mediated post-transcriptional gene silencing)<br />
* BP: GO:0000512 lncRNA-mediated post-transcriptional gene silencing<br />
<br />
=== mRNA translation repression ===<br />
<br />
Figure 2m, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: lncRNAs regulate translation. Association of lincRNA-p21 (linc-p21) with HuR favours the recruitment of let-7/Ago2, leading to its destabilization. In the absence of HuR, lincRNA-p21 identifies mRNA targets to repress their translation by recruiting the translation repressor Rck129. RISC, RNA-induced silencing complex.<br />
<br />
LncRNA annotations:<br />
* MF: GO:1903231 mRNA base-pairing translational repressor activity + additional information (eg part_of GO:0000512 lncRNA-mediated post-transcriptional gene silencing)<br />
* BP: GO:0000512 lncRNA-mediated post-transcriptional gene silencing<br />
<br />
=== regulation of post-translational modifications ===<br />
<br />
Figure 2n, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: lncRNAs modulate post-translational modifications. Lnc-DC directly interacts with STAT3 to prevent its dephosphorylation by SHP1 (PTPN6).<br />
(From PMID:31857450: Phosphorylated STAT3 translocates in to the nucleus and activates transcription involved in dendritic cell differentiation)<br />
<br />
LncRNA annotations URS00007B42BD_9606 (GenBank:KJ020271) and URS00007B3652_9606 (GenBank:KJ020272) from PMID:31857450 'The STAT3-binding long noncoding RNA lnc-DC controls human dendritic cell differentiation'<br />
* MF: GO:0019212 phosphatase inhibitor activity<br />
**has_input UniProtKB:P29350 (PTPN6)<br />
* MF: GO:0097677 STAT family protein binding<br />
**has_input UniProtKB:P40763 (STAT3)<br />
<br />
BP terms to describe regulation of pathway and involvement in processes:<br />
* BP: GO:0046427 positive regulation of receptor signaling pathway via JAK-STAT<br />
* BP: GO0097028 dendritic cell differentiation<br />
<br />
<br />
[[Category:Annotation Guidelines]]</div>Hla28https://wiki.geneontology.org/index.php?title=LncRNA_GO_annotation_manual&diff=86633LncRNA GO annotation manual2024-03-06T14:04:30Z<p>Hla28: /* regulation of post-translational modifications */</p>
<hr />
<div>LncRNAs have multiple and varied activities (see [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]] which describes 13 roles of lncRNAs), these guidelines are suggestions for the curation of some of these lncRNAs. These were discussed [https://github.com/geneontology/go-ontology/issues/23028 here].<br />
<br />
===Decision tree to assist with curation of lncRNA:miRNA interactions===<br />
<br />
These guidelines are for the curation of lncRNAs that bind to miRNA and prevent miRNA activity. These lncRNAs are often described as sponge lncRNAs.<br />
<br />
Link to LncRNA_Decision_Tree pdf[[https://wiki.geneontology.org/images/e/e4/LncRNA_Decision_Tree.pdf]]<br />
<br />
[[File:LncRNA Decision Tree.jpg|960x540px]]<br />
<br />
'''Decision Tree for the GO terms and annotation extensions used for capturing targets of lncRNAs.''' The types of evidence in the blue boxes are described further in the text. Information about the cell or tissue that the interaction occurs in can be captured for example in the annotation extension field using: occurs_in (insert cell ontology ID and/or UBERON ID based on cell and/or tissue type respectively). This information can be included when inhibition of the lncRNA leads to an increase in the endogenous miRNA (or decrease in the miRNA target protein level). Slightly weaker evidence to support inclusion of the cell or tissue information would be evidence that the lncRNA is expressed in these cells/this tissue AND that the authors are confident that the lncRNA target is also being regulated in these cells/this tissue. For example, when the addition of the lncRNA leads to a decrease in the endogenous miRNA or increase in the endogenous protein level.<br />
<br />
'''Note:''' to be able to indicate any target in a GO annotation, the prediction evidence does not need to be in the paper you are annotating, it could be from another paper or a prediction database. When looking at predictions or validations in a prediction database, it is recommended to check the references cited for the target as they may serve as a good source of experimental annotation. Additionally, it has been found that some of the cited papers do not support the validation of the targets. Annotations to “miRNA inhibitor activity via base pairing” (GO:0140869) should ONLY be made from the paper containing the experimental evidence, however it is acceptable to indicate in the annotation extension of a “gene silencing by miRNA” annotation that the target of gene silencing is direct (by using ''has_input'') if the evidence for binding is in another paper.<br />
<br />
===Random inactivation of X chromosome===<br />
<br />
Figure 2b [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: Xist modulates inactive X chromosome (Xi) architecture during X chromosome inactivation (XCI) by recruiting Xi to associate with the lamin B receptor (LBR) at the nuclear lamina to silence transcription.<br />
<br />
LncRNA (Xist) Annotations:<br />
* MF: GO:0140463 chromatin-protein adaptor activity + appropriate information etc (eg part_of GO:0060820 inactivation of X chromosome by heterochromatin formation)<br />
* BF: GO:0060816 random inactivation of X chromosome<br />
<br />
=== DNA-DNA tethering activity ===<br />
<br />
Figure 2c [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: Firre transcripts localize to their transcription site and five additional autosomal chromosomal loci in trans to affect interactions between distant genomic regions.<br />
<br />
LncRNA (Firre) annotations:<br />
* MF: GO:0106260 DNA-DNA tethering activity + appropriate information etc (eg part_of GO:0006325 chromatin organization)<br />
* BP: GO:0006325 chromatin organization<br />
<br />
=== Promoter-enhancer loop anchoring activity ===<br />
<br />
Figure 2d [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: CCAT1-L accumulates in cis to modulate chromatin loops between enhancers and the promoter of MYC.<br />
<br />
LncRNA (CCAT1-L) annotations:<br />
* MF: GO:0140585 promoter-enhancer loop anchoring activity + appropriate information etc (eg part_of GO:0140588 chromatin looping)<br />
* BP: GO:0140588 chromatin looping<br />
<br />
=== Regulation of chromatin accessibility ===<br />
<br />
Figure 2e [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: lncRNAs regulate chromatin accessibility. Left, Xist recruits HDAC1-associated repressor protein (SHARP), silencing the mediator for retinoid and thyroid hormone receptor (SMART) and HDAC3 to silence Xi. Right, Mhrt prevents SWI/SNF binding to corresponding DNA loci.<br />
<br />
LncRNA (Xist) annotations:<br />
* MF: GO:0030674 protein-macromolecule adaptor activity + appropriate information (eg part_of GO:0006338 chromatin remodeling)<br />
* BP: GO:0006338 chromatin remodeling<br />
<br />
LncRNA (Mhrt) annotations based on [[https://pubmed.ncbi.nlm.nih.gov/25119045/ PMID:25119045]]:<br />
* MF: GO:0140311 protein sequestering activity + appropriate information etc (eg has_inputs Brg1/Smarca4, Q3TKT4), part_of GO:0006338 chromatin remodeling)<br />
* BP: GO:0006338 chromatin remodeling<br />
<br />
=== Triplex-Mediated Changes in Chromatin Structure ===<br />
<br />
Figure 2f, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: Khps1 enhances Pol II transcription by forming an R-loop that anchors Khps1-interacting p300/CBP to the SPHK1 promoter.<br />
<br />
LncRNA (Khps1) annotations based on [[https://pubmed.ncbi.nlm.nih.gov/26590717/ PMID: 26590717]]:<br />
<br />
* MF: GO:0030674 protein-macromolecule adaptor activity or GO:0001010 RNA polymerase II sequence-specific DNA-binding transcription factor recruiting activity + appropriate information etc (eg part_of GO:0045944 positive regulation of transcription by RNA polymerase II)<br />
* MF: GO:1990837 sequence-specific double-stranded DNA binding + appropriate information etc (eg part_of GO:0006325 chromatin organization)<br />
* BP: GO:0006325 chromatin organization<br />
* BP: GO:0045944 positive regulation of transcription by RNA polymerase II<br />
<br />
=== RNA polymerase inhibitor activity ===<br />
<br />
Figure 2g, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]:lncRNAs interfere with Pol II transcription machineries both at the initiation (left) and elongation (right) stages.<br />
<br />
LncRNA annotations:<br />
* MF: GO:0140870 RNA polymerase inhibitor activity<br />
* BP:GO:0000122 negative regulation of transcription by RNA polymerase II<br />
<br />
=== repressor of RNA polymerase inhibitor activity ===<br />
<br />
Figure 2h, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: SLERT promotes Pol I transcription by binding DDX21 to alter its conformation, thereby releasing its inhibitory effect on Pol I.<br />
<br />
LncRNA (SLERT) annotations:<br />
* MF: GO:0140871 repressor of RNA polymerase inhibitor activity + appropriate information (eg has_input DDX21)<br />
* BP: GO:0045943 positive regulation of transcription by RNA polymerase I<br />
<br />
=== molecular condensate scaffold activity ===<br />
<br />
Figure 2i, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: NEAT1 is an architectural lncRNA that nucleates paraspeckles. Upon cellular stress, altered NEAT1 transcription and processing lead to changes of paraspeckles. PSP, paraspeckle proteins.<br />
<br />
LncRNA (NEAT1) annotations:<br />
* MF: GO:0140693 molecular condensate scaffold activity + additional information (eg part_of GO:0006325 chromatin organization or GO:0006996 organelle organization)<br />
* BP: GO:0030575 nuclear body organization<br />
<br />
=== miRNA inhibitor activity / sponge ===<br />
<br />
See decision tree above <br />
Figure 2k, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: A regulatory network consisting of different types of ncRNAs. Cyrano, harbouring miR-7 binding sites, targets miR-7 for degradation and prevents miR-7 from repressing its target RNAs including the circRNA Cdr1as.<br />
<br />
LncRNA (Cyrano) annotations: <br />
* MF GO:0140869 miRNA inhibitor activity via base-pairing + additional information (eg has_input miR-7 RNAcentral ID, part_of GO:0000512 lncRNA-mediated post-transcriptional gene silencing)<br />
* BP: GO:0000512 lncRNA-mediated post-transcriptional gene silencing<br />
<br />
=== mRNA degradation ===<br />
<br />
Figure 2l, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: lncRNAs modulate mRNA stability by associating with proteins involved in mRNA degradation. Left, double-stranded RNAs formed by Alu-containing lncRNAs with mRNA 3′ UTRs recruit STAU1 to induce STAU1-mediated mRNA decay (SMD). Right, NORAD stabilizes PUMILIO 1/2 (PUM1/2)-targeted mRNAs via sequestering PUM1/2 from mRNAs.<br />
<br />
LncRNA (NORAD) annotations:<br />
* MF: GO:1903231 mRNA base-pairing translational repressor activity + additional information (eg part_of GO:0000512 lncRNA-mediated post-transcriptional gene silencing)<br />
* BP: GO:0000512 lncRNA-mediated post-transcriptional gene silencing<br />
<br />
=== mRNA translation repression ===<br />
<br />
Figure 2m, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: lncRNAs regulate translation. Association of lincRNA-p21 (linc-p21) with HuR favours the recruitment of let-7/Ago2, leading to its destabilization. In the absence of HuR, lincRNA-p21 identifies mRNA targets to repress their translation by recruiting the translation repressor Rck129. RISC, RNA-induced silencing complex.<br />
<br />
LncRNA annotations:<br />
* MF: GO:1903231 mRNA base-pairing translational repressor activity + additional information (eg part_of GO:0000512 lncRNA-mediated post-transcriptional gene silencing)<br />
* BP: GO:0000512 lncRNA-mediated post-transcriptional gene silencing<br />
<br />
=== regulation of post-translational modifications ===<br />
<br />
Figure 2n, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: lncRNAs modulate post-translational modifications. Lnc-DC directly interacts with STAT3 to prevent its dephosphorylation by SHP1 (PTPN6).<br />
(From PMID:31857450: Phosphorylated STAT3 translocates in to the nucleus and activates transcription involved in dendritic cell differentiation)<br />
<br />
LncRNA annotations URS00007B42BD_9606 (GenBank:KJ020271) and URS00007B3652_9606 (GenBank:KJ020272) from PMID:31857450 'The STAT3-binding long noncoding RNA lnc-DC controls human dendritic cell differentiation'<br />
* MF: GO:0019212 phosphatase inhibitor activity<br />
**has_input UniProtKB:P29350 (PTPN6)<br />
* MF: GO:0097677 STAT family protein binding<br />
**has_input UniProtKB:P40763 (STAT3)<br />
<br />
BP terms to describe regulation of pathway and involvement in processes:<br />
* BP: GO:0046427 positive regulation of receptor signaling pathway via JAK-STAT<br />
* BP: GO0097028 dendritic cell differentiation<br />
<br />
<br />
[[Category:Annotation Guidelines]]</div>Hla28https://wiki.geneontology.org/index.php?title=LncRNA_GO_annotation_manual&diff=86632LncRNA GO annotation manual2024-03-06T13:40:10Z<p>Hla28: /* regulation of post-translational modifications */</p>
<hr />
<div>LncRNAs have multiple and varied activities (see [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]] which describes 13 roles of lncRNAs), these guidelines are suggestions for the curation of some of these lncRNAs. These were discussed [https://github.com/geneontology/go-ontology/issues/23028 here].<br />
<br />
===Decision tree to assist with curation of lncRNA:miRNA interactions===<br />
<br />
These guidelines are for the curation of lncRNAs that bind to miRNA and prevent miRNA activity. These lncRNAs are often described as sponge lncRNAs.<br />
<br />
Link to LncRNA_Decision_Tree pdf[[https://wiki.geneontology.org/images/e/e4/LncRNA_Decision_Tree.pdf]]<br />
<br />
[[File:LncRNA Decision Tree.jpg|960x540px]]<br />
<br />
'''Decision Tree for the GO terms and annotation extensions used for capturing targets of lncRNAs.''' The types of evidence in the blue boxes are described further in the text. Information about the cell or tissue that the interaction occurs in can be captured for example in the annotation extension field using: occurs_in (insert cell ontology ID and/or UBERON ID based on cell and/or tissue type respectively). This information can be included when inhibition of the lncRNA leads to an increase in the endogenous miRNA (or decrease in the miRNA target protein level). Slightly weaker evidence to support inclusion of the cell or tissue information would be evidence that the lncRNA is expressed in these cells/this tissue AND that the authors are confident that the lncRNA target is also being regulated in these cells/this tissue. For example, when the addition of the lncRNA leads to a decrease in the endogenous miRNA or increase in the endogenous protein level.<br />
<br />
'''Note:''' to be able to indicate any target in a GO annotation, the prediction evidence does not need to be in the paper you are annotating, it could be from another paper or a prediction database. When looking at predictions or validations in a prediction database, it is recommended to check the references cited for the target as they may serve as a good source of experimental annotation. Additionally, it has been found that some of the cited papers do not support the validation of the targets. Annotations to “miRNA inhibitor activity via base pairing” (GO:0140869) should ONLY be made from the paper containing the experimental evidence, however it is acceptable to indicate in the annotation extension of a “gene silencing by miRNA” annotation that the target of gene silencing is direct (by using ''has_input'') if the evidence for binding is in another paper.<br />
<br />
===Random inactivation of X chromosome===<br />
<br />
Figure 2b [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: Xist modulates inactive X chromosome (Xi) architecture during X chromosome inactivation (XCI) by recruiting Xi to associate with the lamin B receptor (LBR) at the nuclear lamina to silence transcription.<br />
<br />
LncRNA (Xist) Annotations:<br />
* MF: GO:0140463 chromatin-protein adaptor activity + appropriate information etc (eg part_of GO:0060820 inactivation of X chromosome by heterochromatin formation)<br />
* BF: GO:0060816 random inactivation of X chromosome<br />
<br />
=== DNA-DNA tethering activity ===<br />
<br />
Figure 2c [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: Firre transcripts localize to their transcription site and five additional autosomal chromosomal loci in trans to affect interactions between distant genomic regions.<br />
<br />
LncRNA (Firre) annotations:<br />
* MF: GO:0106260 DNA-DNA tethering activity + appropriate information etc (eg part_of GO:0006325 chromatin organization)<br />
* BP: GO:0006325 chromatin organization<br />
<br />
=== Promoter-enhancer loop anchoring activity ===<br />
<br />
Figure 2d [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: CCAT1-L accumulates in cis to modulate chromatin loops between enhancers and the promoter of MYC.<br />
<br />
LncRNA (CCAT1-L) annotations:<br />
* MF: GO:0140585 promoter-enhancer loop anchoring activity + appropriate information etc (eg part_of GO:0140588 chromatin looping)<br />
* BP: GO:0140588 chromatin looping<br />
<br />
=== Regulation of chromatin accessibility ===<br />
<br />
Figure 2e [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: lncRNAs regulate chromatin accessibility. Left, Xist recruits HDAC1-associated repressor protein (SHARP), silencing the mediator for retinoid and thyroid hormone receptor (SMART) and HDAC3 to silence Xi. Right, Mhrt prevents SWI/SNF binding to corresponding DNA loci.<br />
<br />
LncRNA (Xist) annotations:<br />
* MF: GO:0030674 protein-macromolecule adaptor activity + appropriate information (eg part_of GO:0006338 chromatin remodeling)<br />
* BP: GO:0006338 chromatin remodeling<br />
<br />
LncRNA (Mhrt) annotations based on [[https://pubmed.ncbi.nlm.nih.gov/25119045/ PMID:25119045]]:<br />
* MF: GO:0140311 protein sequestering activity + appropriate information etc (eg has_inputs Brg1/Smarca4, Q3TKT4), part_of GO:0006338 chromatin remodeling)<br />
* BP: GO:0006338 chromatin remodeling<br />
<br />
=== Triplex-Mediated Changes in Chromatin Structure ===<br />
<br />
Figure 2f, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: Khps1 enhances Pol II transcription by forming an R-loop that anchors Khps1-interacting p300/CBP to the SPHK1 promoter.<br />
<br />
LncRNA (Khps1) annotations based on [[https://pubmed.ncbi.nlm.nih.gov/26590717/ PMID: 26590717]]:<br />
<br />
* MF: GO:0030674 protein-macromolecule adaptor activity or GO:0001010 RNA polymerase II sequence-specific DNA-binding transcription factor recruiting activity + appropriate information etc (eg part_of GO:0045944 positive regulation of transcription by RNA polymerase II)<br />
* MF: GO:1990837 sequence-specific double-stranded DNA binding + appropriate information etc (eg part_of GO:0006325 chromatin organization)<br />
* BP: GO:0006325 chromatin organization<br />
* BP: GO:0045944 positive regulation of transcription by RNA polymerase II<br />
<br />
=== RNA polymerase inhibitor activity ===<br />
<br />
Figure 2g, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]:lncRNAs interfere with Pol II transcription machineries both at the initiation (left) and elongation (right) stages.<br />
<br />
LncRNA annotations:<br />
* MF: GO:0140870 RNA polymerase inhibitor activity<br />
* BP:GO:0000122 negative regulation of transcription by RNA polymerase II<br />
<br />
=== repressor of RNA polymerase inhibitor activity ===<br />
<br />
Figure 2h, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: SLERT promotes Pol I transcription by binding DDX21 to alter its conformation, thereby releasing its inhibitory effect on Pol I.<br />
<br />
LncRNA (SLERT) annotations:<br />
* MF: GO:0140871 repressor of RNA polymerase inhibitor activity + appropriate information (eg has_input DDX21)<br />
* BP: GO:0045943 positive regulation of transcription by RNA polymerase I<br />
<br />
=== molecular condensate scaffold activity ===<br />
<br />
Figure 2i, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: NEAT1 is an architectural lncRNA that nucleates paraspeckles. Upon cellular stress, altered NEAT1 transcription and processing lead to changes of paraspeckles. PSP, paraspeckle proteins.<br />
<br />
LncRNA (NEAT1) annotations:<br />
* MF: GO:0140693 molecular condensate scaffold activity + additional information (eg part_of GO:0006325 chromatin organization or GO:0006996 organelle organization)<br />
* BP: GO:0030575 nuclear body organization<br />
<br />
=== miRNA inhibitor activity / sponge ===<br />
<br />
See decision tree above <br />
Figure 2k, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: A regulatory network consisting of different types of ncRNAs. Cyrano, harbouring miR-7 binding sites, targets miR-7 for degradation and prevents miR-7 from repressing its target RNAs including the circRNA Cdr1as.<br />
<br />
LncRNA (Cyrano) annotations: <br />
* MF GO:0140869 miRNA inhibitor activity via base-pairing + additional information (eg has_input miR-7 RNAcentral ID, part_of GO:0000512 lncRNA-mediated post-transcriptional gene silencing)<br />
* BP: GO:0000512 lncRNA-mediated post-transcriptional gene silencing<br />
<br />
=== mRNA degradation ===<br />
<br />
Figure 2l, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: lncRNAs modulate mRNA stability by associating with proteins involved in mRNA degradation. Left, double-stranded RNAs formed by Alu-containing lncRNAs with mRNA 3′ UTRs recruit STAU1 to induce STAU1-mediated mRNA decay (SMD). Right, NORAD stabilizes PUMILIO 1/2 (PUM1/2)-targeted mRNAs via sequestering PUM1/2 from mRNAs.<br />
<br />
LncRNA (NORAD) annotations:<br />
* MF: GO:1903231 mRNA base-pairing translational repressor activity + additional information (eg part_of GO:0000512 lncRNA-mediated post-transcriptional gene silencing)<br />
* BP: GO:0000512 lncRNA-mediated post-transcriptional gene silencing<br />
<br />
=== mRNA translation repression ===<br />
<br />
Figure 2m, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: lncRNAs regulate translation. Association of lincRNA-p21 (linc-p21) with HuR favours the recruitment of let-7/Ago2, leading to its destabilization. In the absence of HuR, lincRNA-p21 identifies mRNA targets to repress their translation by recruiting the translation repressor Rck129. RISC, RNA-induced silencing complex.<br />
<br />
LncRNA annotations:<br />
* MF: GO:1903231 mRNA base-pairing translational repressor activity + additional information (eg part_of GO:0000512 lncRNA-mediated post-transcriptional gene silencing)<br />
* BP: GO:0000512 lncRNA-mediated post-transcriptional gene silencing<br />
<br />
=== regulation of post-translational modifications ===<br />
<br />
Figure 2n, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: lncRNAs modulate post-translational modifications. Lnc-DC directly interacts with STAT3 to prevent its dephosphorylation by SHP1 (PTPN6).<br />
(From PMID:31857450: Phosphorylated STAT3 translocates in to the nucleus and activates transcription involved in dendritic cell differentiation)<br />
<br />
LncRNA annotations: URS00007B42BD_9606 (lnc-DC; HSALNT0243356) from PMID:31857450 'The STAT3-binding long noncoding RNA lnc-DC controls human dendritic cell differentiation'<br />
* MF: GO:0019212 phosphatase inhibitor activity<br />
**has_input UniProtKB:P29350 (PTPN6)<br />
* MF: GO:0097677 STAT family protein binding<br />
**has_input UniProtKB:P40763 (STAT3)<br />
<br />
BP terms to describe regulation of pathway and involvement in processes:<br />
* BP: GO:0046427 positive regulation of receptor signaling pathway via JAK-STAT<br />
* BP: GO0097028 dendritic cell differentiation<br />
<br />
<br />
[[Category:Annotation Guidelines]]</div>Hla28https://wiki.geneontology.org/index.php?title=LncRNA_GO_annotation_manual&diff=86631LncRNA GO annotation manual2024-03-06T13:39:24Z<p>Hla28: /* regulation of post-translational modifications */</p>
<hr />
<div>LncRNAs have multiple and varied activities (see [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]] which describes 13 roles of lncRNAs), these guidelines are suggestions for the curation of some of these lncRNAs. These were discussed [https://github.com/geneontology/go-ontology/issues/23028 here].<br />
<br />
===Decision tree to assist with curation of lncRNA:miRNA interactions===<br />
<br />
These guidelines are for the curation of lncRNAs that bind to miRNA and prevent miRNA activity. These lncRNAs are often described as sponge lncRNAs.<br />
<br />
Link to LncRNA_Decision_Tree pdf[[https://wiki.geneontology.org/images/e/e4/LncRNA_Decision_Tree.pdf]]<br />
<br />
[[File:LncRNA Decision Tree.jpg|960x540px]]<br />
<br />
'''Decision Tree for the GO terms and annotation extensions used for capturing targets of lncRNAs.''' The types of evidence in the blue boxes are described further in the text. Information about the cell or tissue that the interaction occurs in can be captured for example in the annotation extension field using: occurs_in (insert cell ontology ID and/or UBERON ID based on cell and/or tissue type respectively). This information can be included when inhibition of the lncRNA leads to an increase in the endogenous miRNA (or decrease in the miRNA target protein level). Slightly weaker evidence to support inclusion of the cell or tissue information would be evidence that the lncRNA is expressed in these cells/this tissue AND that the authors are confident that the lncRNA target is also being regulated in these cells/this tissue. For example, when the addition of the lncRNA leads to a decrease in the endogenous miRNA or increase in the endogenous protein level.<br />
<br />
'''Note:''' to be able to indicate any target in a GO annotation, the prediction evidence does not need to be in the paper you are annotating, it could be from another paper or a prediction database. When looking at predictions or validations in a prediction database, it is recommended to check the references cited for the target as they may serve as a good source of experimental annotation. Additionally, it has been found that some of the cited papers do not support the validation of the targets. Annotations to “miRNA inhibitor activity via base pairing” (GO:0140869) should ONLY be made from the paper containing the experimental evidence, however it is acceptable to indicate in the annotation extension of a “gene silencing by miRNA” annotation that the target of gene silencing is direct (by using ''has_input'') if the evidence for binding is in another paper.<br />
<br />
===Random inactivation of X chromosome===<br />
<br />
Figure 2b [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: Xist modulates inactive X chromosome (Xi) architecture during X chromosome inactivation (XCI) by recruiting Xi to associate with the lamin B receptor (LBR) at the nuclear lamina to silence transcription.<br />
<br />
LncRNA (Xist) Annotations:<br />
* MF: GO:0140463 chromatin-protein adaptor activity + appropriate information etc (eg part_of GO:0060820 inactivation of X chromosome by heterochromatin formation)<br />
* BF: GO:0060816 random inactivation of X chromosome<br />
<br />
=== DNA-DNA tethering activity ===<br />
<br />
Figure 2c [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: Firre transcripts localize to their transcription site and five additional autosomal chromosomal loci in trans to affect interactions between distant genomic regions.<br />
<br />
LncRNA (Firre) annotations:<br />
* MF: GO:0106260 DNA-DNA tethering activity + appropriate information etc (eg part_of GO:0006325 chromatin organization)<br />
* BP: GO:0006325 chromatin organization<br />
<br />
=== Promoter-enhancer loop anchoring activity ===<br />
<br />
Figure 2d [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: CCAT1-L accumulates in cis to modulate chromatin loops between enhancers and the promoter of MYC.<br />
<br />
LncRNA (CCAT1-L) annotations:<br />
* MF: GO:0140585 promoter-enhancer loop anchoring activity + appropriate information etc (eg part_of GO:0140588 chromatin looping)<br />
* BP: GO:0140588 chromatin looping<br />
<br />
=== Regulation of chromatin accessibility ===<br />
<br />
Figure 2e [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: lncRNAs regulate chromatin accessibility. Left, Xist recruits HDAC1-associated repressor protein (SHARP), silencing the mediator for retinoid and thyroid hormone receptor (SMART) and HDAC3 to silence Xi. Right, Mhrt prevents SWI/SNF binding to corresponding DNA loci.<br />
<br />
LncRNA (Xist) annotations:<br />
* MF: GO:0030674 protein-macromolecule adaptor activity + appropriate information (eg part_of GO:0006338 chromatin remodeling)<br />
* BP: GO:0006338 chromatin remodeling<br />
<br />
LncRNA (Mhrt) annotations based on [[https://pubmed.ncbi.nlm.nih.gov/25119045/ PMID:25119045]]:<br />
* MF: GO:0140311 protein sequestering activity + appropriate information etc (eg has_inputs Brg1/Smarca4, Q3TKT4), part_of GO:0006338 chromatin remodeling)<br />
* BP: GO:0006338 chromatin remodeling<br />
<br />
=== Triplex-Mediated Changes in Chromatin Structure ===<br />
<br />
Figure 2f, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: Khps1 enhances Pol II transcription by forming an R-loop that anchors Khps1-interacting p300/CBP to the SPHK1 promoter.<br />
<br />
LncRNA (Khps1) annotations based on [[https://pubmed.ncbi.nlm.nih.gov/26590717/ PMID: 26590717]]:<br />
<br />
* MF: GO:0030674 protein-macromolecule adaptor activity or GO:0001010 RNA polymerase II sequence-specific DNA-binding transcription factor recruiting activity + appropriate information etc (eg part_of GO:0045944 positive regulation of transcription by RNA polymerase II)<br />
* MF: GO:1990837 sequence-specific double-stranded DNA binding + appropriate information etc (eg part_of GO:0006325 chromatin organization)<br />
* BP: GO:0006325 chromatin organization<br />
* BP: GO:0045944 positive regulation of transcription by RNA polymerase II<br />
<br />
=== RNA polymerase inhibitor activity ===<br />
<br />
Figure 2g, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]:lncRNAs interfere with Pol II transcription machineries both at the initiation (left) and elongation (right) stages.<br />
<br />
LncRNA annotations:<br />
* MF: GO:0140870 RNA polymerase inhibitor activity<br />
* BP:GO:0000122 negative regulation of transcription by RNA polymerase II<br />
<br />
=== repressor of RNA polymerase inhibitor activity ===<br />
<br />
Figure 2h, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: SLERT promotes Pol I transcription by binding DDX21 to alter its conformation, thereby releasing its inhibitory effect on Pol I.<br />
<br />
LncRNA (SLERT) annotations:<br />
* MF: GO:0140871 repressor of RNA polymerase inhibitor activity + appropriate information (eg has_input DDX21)<br />
* BP: GO:0045943 positive regulation of transcription by RNA polymerase I<br />
<br />
=== molecular condensate scaffold activity ===<br />
<br />
Figure 2i, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: NEAT1 is an architectural lncRNA that nucleates paraspeckles. Upon cellular stress, altered NEAT1 transcription and processing lead to changes of paraspeckles. PSP, paraspeckle proteins.<br />
<br />
LncRNA (NEAT1) annotations:<br />
* MF: GO:0140693 molecular condensate scaffold activity + additional information (eg part_of GO:0006325 chromatin organization or GO:0006996 organelle organization)<br />
* BP: GO:0030575 nuclear body organization<br />
<br />
=== miRNA inhibitor activity / sponge ===<br />
<br />
See decision tree above <br />
Figure 2k, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: A regulatory network consisting of different types of ncRNAs. Cyrano, harbouring miR-7 binding sites, targets miR-7 for degradation and prevents miR-7 from repressing its target RNAs including the circRNA Cdr1as.<br />
<br />
LncRNA (Cyrano) annotations: <br />
* MF GO:0140869 miRNA inhibitor activity via base-pairing + additional information (eg has_input miR-7 RNAcentral ID, part_of GO:0000512 lncRNA-mediated post-transcriptional gene silencing)<br />
* BP: GO:0000512 lncRNA-mediated post-transcriptional gene silencing<br />
<br />
=== mRNA degradation ===<br />
<br />
Figure 2l, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: lncRNAs modulate mRNA stability by associating with proteins involved in mRNA degradation. Left, double-stranded RNAs formed by Alu-containing lncRNAs with mRNA 3′ UTRs recruit STAU1 to induce STAU1-mediated mRNA decay (SMD). Right, NORAD stabilizes PUMILIO 1/2 (PUM1/2)-targeted mRNAs via sequestering PUM1/2 from mRNAs.<br />
<br />
LncRNA (NORAD) annotations:<br />
* MF: GO:1903231 mRNA base-pairing translational repressor activity + additional information (eg part_of GO:0000512 lncRNA-mediated post-transcriptional gene silencing)<br />
* BP: GO:0000512 lncRNA-mediated post-transcriptional gene silencing<br />
<br />
=== mRNA translation repression ===<br />
<br />
Figure 2m, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: lncRNAs regulate translation. Association of lincRNA-p21 (linc-p21) with HuR favours the recruitment of let-7/Ago2, leading to its destabilization. In the absence of HuR, lincRNA-p21 identifies mRNA targets to repress their translation by recruiting the translation repressor Rck129. RISC, RNA-induced silencing complex.<br />
<br />
LncRNA annotations:<br />
* MF: GO:1903231 mRNA base-pairing translational repressor activity + additional information (eg part_of GO:0000512 lncRNA-mediated post-transcriptional gene silencing)<br />
* BP: GO:0000512 lncRNA-mediated post-transcriptional gene silencing<br />
<br />
=== regulation of post-translational modifications ===<br />
<br />
Figure 2n, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: lncRNAs modulate post-translational modifications. Lnc-DC directly interacts with STAT3 to prevent its dephosphorylation by SHP1 (PTPN6).<br />
(From PMID:31857450: Phosphorylated STAT3 translocates in to the nucleus and activates transcription involved in dendritic cell differentiation)<br />
<br />
LncRNA annotations:URS00007B42BD_9606 (lnc-DC; HSALNT0243356) from PMID:31857450 'The STAT3-binding long noncoding RNA lnc-DC controls human dendritic cell differentiation'<br />
* MF: GO:0019212 phosphatase inhibitor activity<br />
**has_input UniProtKB:P29350 (PTPN6)<br />
* MF: GO:0097677 STAT family protein binding<br />
**has_input UniProtKB:P40763 (STAT3)<br />
<br />
BP terms to describe regulation of pathway and involvement in processes:<br />
* BP: GO:0046427 positive regulation of receptor signaling pathway via JAK-STAT<br />
* BP: GO0097028 dendritic cell differentiation<br />
<br />
<br />
[[Category:Annotation Guidelines]]</div>Hla28https://wiki.geneontology.org/index.php?title=LncRNA_GO_annotation_manual&diff=86630LncRNA GO annotation manual2024-03-06T13:39:16Z<p>Hla28: /* regulation of post-translational modifications */</p>
<hr />
<div>LncRNAs have multiple and varied activities (see [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]] which describes 13 roles of lncRNAs), these guidelines are suggestions for the curation of some of these lncRNAs. These were discussed [https://github.com/geneontology/go-ontology/issues/23028 here].<br />
<br />
===Decision tree to assist with curation of lncRNA:miRNA interactions===<br />
<br />
These guidelines are for the curation of lncRNAs that bind to miRNA and prevent miRNA activity. These lncRNAs are often described as sponge lncRNAs.<br />
<br />
Link to LncRNA_Decision_Tree pdf[[https://wiki.geneontology.org/images/e/e4/LncRNA_Decision_Tree.pdf]]<br />
<br />
[[File:LncRNA Decision Tree.jpg|960x540px]]<br />
<br />
'''Decision Tree for the GO terms and annotation extensions used for capturing targets of lncRNAs.''' The types of evidence in the blue boxes are described further in the text. Information about the cell or tissue that the interaction occurs in can be captured for example in the annotation extension field using: occurs_in (insert cell ontology ID and/or UBERON ID based on cell and/or tissue type respectively). This information can be included when inhibition of the lncRNA leads to an increase in the endogenous miRNA (or decrease in the miRNA target protein level). Slightly weaker evidence to support inclusion of the cell or tissue information would be evidence that the lncRNA is expressed in these cells/this tissue AND that the authors are confident that the lncRNA target is also being regulated in these cells/this tissue. For example, when the addition of the lncRNA leads to a decrease in the endogenous miRNA or increase in the endogenous protein level.<br />
<br />
'''Note:''' to be able to indicate any target in a GO annotation, the prediction evidence does not need to be in the paper you are annotating, it could be from another paper or a prediction database. When looking at predictions or validations in a prediction database, it is recommended to check the references cited for the target as they may serve as a good source of experimental annotation. Additionally, it has been found that some of the cited papers do not support the validation of the targets. Annotations to “miRNA inhibitor activity via base pairing” (GO:0140869) should ONLY be made from the paper containing the experimental evidence, however it is acceptable to indicate in the annotation extension of a “gene silencing by miRNA” annotation that the target of gene silencing is direct (by using ''has_input'') if the evidence for binding is in another paper.<br />
<br />
===Random inactivation of X chromosome===<br />
<br />
Figure 2b [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: Xist modulates inactive X chromosome (Xi) architecture during X chromosome inactivation (XCI) by recruiting Xi to associate with the lamin B receptor (LBR) at the nuclear lamina to silence transcription.<br />
<br />
LncRNA (Xist) Annotations:<br />
* MF: GO:0140463 chromatin-protein adaptor activity + appropriate information etc (eg part_of GO:0060820 inactivation of X chromosome by heterochromatin formation)<br />
* BF: GO:0060816 random inactivation of X chromosome<br />
<br />
=== DNA-DNA tethering activity ===<br />
<br />
Figure 2c [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: Firre transcripts localize to their transcription site and five additional autosomal chromosomal loci in trans to affect interactions between distant genomic regions.<br />
<br />
LncRNA (Firre) annotations:<br />
* MF: GO:0106260 DNA-DNA tethering activity + appropriate information etc (eg part_of GO:0006325 chromatin organization)<br />
* BP: GO:0006325 chromatin organization<br />
<br />
=== Promoter-enhancer loop anchoring activity ===<br />
<br />
Figure 2d [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: CCAT1-L accumulates in cis to modulate chromatin loops between enhancers and the promoter of MYC.<br />
<br />
LncRNA (CCAT1-L) annotations:<br />
* MF: GO:0140585 promoter-enhancer loop anchoring activity + appropriate information etc (eg part_of GO:0140588 chromatin looping)<br />
* BP: GO:0140588 chromatin looping<br />
<br />
=== Regulation of chromatin accessibility ===<br />
<br />
Figure 2e [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: lncRNAs regulate chromatin accessibility. Left, Xist recruits HDAC1-associated repressor protein (SHARP), silencing the mediator for retinoid and thyroid hormone receptor (SMART) and HDAC3 to silence Xi. Right, Mhrt prevents SWI/SNF binding to corresponding DNA loci.<br />
<br />
LncRNA (Xist) annotations:<br />
* MF: GO:0030674 protein-macromolecule adaptor activity + appropriate information (eg part_of GO:0006338 chromatin remodeling)<br />
* BP: GO:0006338 chromatin remodeling<br />
<br />
LncRNA (Mhrt) annotations based on [[https://pubmed.ncbi.nlm.nih.gov/25119045/ PMID:25119045]]:<br />
* MF: GO:0140311 protein sequestering activity + appropriate information etc (eg has_inputs Brg1/Smarca4, Q3TKT4), part_of GO:0006338 chromatin remodeling)<br />
* BP: GO:0006338 chromatin remodeling<br />
<br />
=== Triplex-Mediated Changes in Chromatin Structure ===<br />
<br />
Figure 2f, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: Khps1 enhances Pol II transcription by forming an R-loop that anchors Khps1-interacting p300/CBP to the SPHK1 promoter.<br />
<br />
LncRNA (Khps1) annotations based on [[https://pubmed.ncbi.nlm.nih.gov/26590717/ PMID: 26590717]]:<br />
<br />
* MF: GO:0030674 protein-macromolecule adaptor activity or GO:0001010 RNA polymerase II sequence-specific DNA-binding transcription factor recruiting activity + appropriate information etc (eg part_of GO:0045944 positive regulation of transcription by RNA polymerase II)<br />
* MF: GO:1990837 sequence-specific double-stranded DNA binding + appropriate information etc (eg part_of GO:0006325 chromatin organization)<br />
* BP: GO:0006325 chromatin organization<br />
* BP: GO:0045944 positive regulation of transcription by RNA polymerase II<br />
<br />
=== RNA polymerase inhibitor activity ===<br />
<br />
Figure 2g, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]:lncRNAs interfere with Pol II transcription machineries both at the initiation (left) and elongation (right) stages.<br />
<br />
LncRNA annotations:<br />
* MF: GO:0140870 RNA polymerase inhibitor activity<br />
* BP:GO:0000122 negative regulation of transcription by RNA polymerase II<br />
<br />
=== repressor of RNA polymerase inhibitor activity ===<br />
<br />
Figure 2h, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: SLERT promotes Pol I transcription by binding DDX21 to alter its conformation, thereby releasing its inhibitory effect on Pol I.<br />
<br />
LncRNA (SLERT) annotations:<br />
* MF: GO:0140871 repressor of RNA polymerase inhibitor activity + appropriate information (eg has_input DDX21)<br />
* BP: GO:0045943 positive regulation of transcription by RNA polymerase I<br />
<br />
=== molecular condensate scaffold activity ===<br />
<br />
Figure 2i, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: NEAT1 is an architectural lncRNA that nucleates paraspeckles. Upon cellular stress, altered NEAT1 transcription and processing lead to changes of paraspeckles. PSP, paraspeckle proteins.<br />
<br />
LncRNA (NEAT1) annotations:<br />
* MF: GO:0140693 molecular condensate scaffold activity + additional information (eg part_of GO:0006325 chromatin organization or GO:0006996 organelle organization)<br />
* BP: GO:0030575 nuclear body organization<br />
<br />
=== miRNA inhibitor activity / sponge ===<br />
<br />
See decision tree above <br />
Figure 2k, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: A regulatory network consisting of different types of ncRNAs. Cyrano, harbouring miR-7 binding sites, targets miR-7 for degradation and prevents miR-7 from repressing its target RNAs including the circRNA Cdr1as.<br />
<br />
LncRNA (Cyrano) annotations: <br />
* MF GO:0140869 miRNA inhibitor activity via base-pairing + additional information (eg has_input miR-7 RNAcentral ID, part_of GO:0000512 lncRNA-mediated post-transcriptional gene silencing)<br />
* BP: GO:0000512 lncRNA-mediated post-transcriptional gene silencing<br />
<br />
=== mRNA degradation ===<br />
<br />
Figure 2l, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: lncRNAs modulate mRNA stability by associating with proteins involved in mRNA degradation. Left, double-stranded RNAs formed by Alu-containing lncRNAs with mRNA 3′ UTRs recruit STAU1 to induce STAU1-mediated mRNA decay (SMD). Right, NORAD stabilizes PUMILIO 1/2 (PUM1/2)-targeted mRNAs via sequestering PUM1/2 from mRNAs.<br />
<br />
LncRNA (NORAD) annotations:<br />
* MF: GO:1903231 mRNA base-pairing translational repressor activity + additional information (eg part_of GO:0000512 lncRNA-mediated post-transcriptional gene silencing)<br />
* BP: GO:0000512 lncRNA-mediated post-transcriptional gene silencing<br />
<br />
=== mRNA translation repression ===<br />
<br />
Figure 2m, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: lncRNAs regulate translation. Association of lincRNA-p21 (linc-p21) with HuR favours the recruitment of let-7/Ago2, leading to its destabilization. In the absence of HuR, lincRNA-p21 identifies mRNA targets to repress their translation by recruiting the translation repressor Rck129. RISC, RNA-induced silencing complex.<br />
<br />
LncRNA annotations:<br />
* MF: GO:1903231 mRNA base-pairing translational repressor activity + additional information (eg part_of GO:0000512 lncRNA-mediated post-transcriptional gene silencing)<br />
* BP: GO:0000512 lncRNA-mediated post-transcriptional gene silencing<br />
<br />
=== regulation of post-translational modifications ===<br />
<br />
Figure 2n, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: lncRNAs modulate post-translational modifications. Lnc-DC directly interacts with STAT3 to prevent its dephosphorylation by SHP1 (PTPN6).<br />
(From PMID:31857450: Phosphorylated STAT3 translocates in to the nucleus and activates transcription involved in dendritic cell differentiation)<br />
<br />
LncRNA annotations:URS00007B42BD_9606 (lnc-DC; HSALNT0243356) from PMID:31857450 'The STAT3-binding long noncoding RNA lnc-DC controls human dendritic cell differentiation'<br />
* MF: GO:0019212 phosphatase inhibitor activity<br />
**has_input UniProtKB:P29350 (PTPN6)<br />
* MF: GO:0097677 STAT family protein binding<br />
**has_input UniProtKB:P40763 (STAT3)<br />
<br />
BP terms to describe regulation of pathway and involvement in processes:<br />
* BP: GO:0046427 positive regulation of receptor signaling pathway via JAK-STAT<br />
*BP: GO0097028 dendritic cell differentiation<br />
<br />
<br />
[[Category:Annotation Guidelines]]</div>Hla28https://wiki.geneontology.org/index.php?title=LncRNA_GO_annotation_manual&diff=86629LncRNA GO annotation manual2024-03-06T13:38:56Z<p>Hla28: /* regulation of post-translational modifications */</p>
<hr />
<div>LncRNAs have multiple and varied activities (see [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]] which describes 13 roles of lncRNAs), these guidelines are suggestions for the curation of some of these lncRNAs. These were discussed [https://github.com/geneontology/go-ontology/issues/23028 here].<br />
<br />
===Decision tree to assist with curation of lncRNA:miRNA interactions===<br />
<br />
These guidelines are for the curation of lncRNAs that bind to miRNA and prevent miRNA activity. These lncRNAs are often described as sponge lncRNAs.<br />
<br />
Link to LncRNA_Decision_Tree pdf[[https://wiki.geneontology.org/images/e/e4/LncRNA_Decision_Tree.pdf]]<br />
<br />
[[File:LncRNA Decision Tree.jpg|960x540px]]<br />
<br />
'''Decision Tree for the GO terms and annotation extensions used for capturing targets of lncRNAs.''' The types of evidence in the blue boxes are described further in the text. Information about the cell or tissue that the interaction occurs in can be captured for example in the annotation extension field using: occurs_in (insert cell ontology ID and/or UBERON ID based on cell and/or tissue type respectively). This information can be included when inhibition of the lncRNA leads to an increase in the endogenous miRNA (or decrease in the miRNA target protein level). Slightly weaker evidence to support inclusion of the cell or tissue information would be evidence that the lncRNA is expressed in these cells/this tissue AND that the authors are confident that the lncRNA target is also being regulated in these cells/this tissue. For example, when the addition of the lncRNA leads to a decrease in the endogenous miRNA or increase in the endogenous protein level.<br />
<br />
'''Note:''' to be able to indicate any target in a GO annotation, the prediction evidence does not need to be in the paper you are annotating, it could be from another paper or a prediction database. When looking at predictions or validations in a prediction database, it is recommended to check the references cited for the target as they may serve as a good source of experimental annotation. Additionally, it has been found that some of the cited papers do not support the validation of the targets. Annotations to “miRNA inhibitor activity via base pairing” (GO:0140869) should ONLY be made from the paper containing the experimental evidence, however it is acceptable to indicate in the annotation extension of a “gene silencing by miRNA” annotation that the target of gene silencing is direct (by using ''has_input'') if the evidence for binding is in another paper.<br />
<br />
===Random inactivation of X chromosome===<br />
<br />
Figure 2b [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: Xist modulates inactive X chromosome (Xi) architecture during X chromosome inactivation (XCI) by recruiting Xi to associate with the lamin B receptor (LBR) at the nuclear lamina to silence transcription.<br />
<br />
LncRNA (Xist) Annotations:<br />
* MF: GO:0140463 chromatin-protein adaptor activity + appropriate information etc (eg part_of GO:0060820 inactivation of X chromosome by heterochromatin formation)<br />
* BF: GO:0060816 random inactivation of X chromosome<br />
<br />
=== DNA-DNA tethering activity ===<br />
<br />
Figure 2c [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: Firre transcripts localize to their transcription site and five additional autosomal chromosomal loci in trans to affect interactions between distant genomic regions.<br />
<br />
LncRNA (Firre) annotations:<br />
* MF: GO:0106260 DNA-DNA tethering activity + appropriate information etc (eg part_of GO:0006325 chromatin organization)<br />
* BP: GO:0006325 chromatin organization<br />
<br />
=== Promoter-enhancer loop anchoring activity ===<br />
<br />
Figure 2d [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: CCAT1-L accumulates in cis to modulate chromatin loops between enhancers and the promoter of MYC.<br />
<br />
LncRNA (CCAT1-L) annotations:<br />
* MF: GO:0140585 promoter-enhancer loop anchoring activity + appropriate information etc (eg part_of GO:0140588 chromatin looping)<br />
* BP: GO:0140588 chromatin looping<br />
<br />
=== Regulation of chromatin accessibility ===<br />
<br />
Figure 2e [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: lncRNAs regulate chromatin accessibility. Left, Xist recruits HDAC1-associated repressor protein (SHARP), silencing the mediator for retinoid and thyroid hormone receptor (SMART) and HDAC3 to silence Xi. Right, Mhrt prevents SWI/SNF binding to corresponding DNA loci.<br />
<br />
LncRNA (Xist) annotations:<br />
* MF: GO:0030674 protein-macromolecule adaptor activity + appropriate information (eg part_of GO:0006338 chromatin remodeling)<br />
* BP: GO:0006338 chromatin remodeling<br />
<br />
LncRNA (Mhrt) annotations based on [[https://pubmed.ncbi.nlm.nih.gov/25119045/ PMID:25119045]]:<br />
* MF: GO:0140311 protein sequestering activity + appropriate information etc (eg has_inputs Brg1/Smarca4, Q3TKT4), part_of GO:0006338 chromatin remodeling)<br />
* BP: GO:0006338 chromatin remodeling<br />
<br />
=== Triplex-Mediated Changes in Chromatin Structure ===<br />
<br />
Figure 2f, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: Khps1 enhances Pol II transcription by forming an R-loop that anchors Khps1-interacting p300/CBP to the SPHK1 promoter.<br />
<br />
LncRNA (Khps1) annotations based on [[https://pubmed.ncbi.nlm.nih.gov/26590717/ PMID: 26590717]]:<br />
<br />
* MF: GO:0030674 protein-macromolecule adaptor activity or GO:0001010 RNA polymerase II sequence-specific DNA-binding transcription factor recruiting activity + appropriate information etc (eg part_of GO:0045944 positive regulation of transcription by RNA polymerase II)<br />
* MF: GO:1990837 sequence-specific double-stranded DNA binding + appropriate information etc (eg part_of GO:0006325 chromatin organization)<br />
* BP: GO:0006325 chromatin organization<br />
* BP: GO:0045944 positive regulation of transcription by RNA polymerase II<br />
<br />
=== RNA polymerase inhibitor activity ===<br />
<br />
Figure 2g, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]:lncRNAs interfere with Pol II transcription machineries both at the initiation (left) and elongation (right) stages.<br />
<br />
LncRNA annotations:<br />
* MF: GO:0140870 RNA polymerase inhibitor activity<br />
* BP:GO:0000122 negative regulation of transcription by RNA polymerase II<br />
<br />
=== repressor of RNA polymerase inhibitor activity ===<br />
<br />
Figure 2h, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: SLERT promotes Pol I transcription by binding DDX21 to alter its conformation, thereby releasing its inhibitory effect on Pol I.<br />
<br />
LncRNA (SLERT) annotations:<br />
* MF: GO:0140871 repressor of RNA polymerase inhibitor activity + appropriate information (eg has_input DDX21)<br />
* BP: GO:0045943 positive regulation of transcription by RNA polymerase I<br />
<br />
=== molecular condensate scaffold activity ===<br />
<br />
Figure 2i, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: NEAT1 is an architectural lncRNA that nucleates paraspeckles. Upon cellular stress, altered NEAT1 transcription and processing lead to changes of paraspeckles. PSP, paraspeckle proteins.<br />
<br />
LncRNA (NEAT1) annotations:<br />
* MF: GO:0140693 molecular condensate scaffold activity + additional information (eg part_of GO:0006325 chromatin organization or GO:0006996 organelle organization)<br />
* BP: GO:0030575 nuclear body organization<br />
<br />
=== miRNA inhibitor activity / sponge ===<br />
<br />
See decision tree above <br />
Figure 2k, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: A regulatory network consisting of different types of ncRNAs. Cyrano, harbouring miR-7 binding sites, targets miR-7 for degradation and prevents miR-7 from repressing its target RNAs including the circRNA Cdr1as.<br />
<br />
LncRNA (Cyrano) annotations: <br />
* MF GO:0140869 miRNA inhibitor activity via base-pairing + additional information (eg has_input miR-7 RNAcentral ID, part_of GO:0000512 lncRNA-mediated post-transcriptional gene silencing)<br />
* BP: GO:0000512 lncRNA-mediated post-transcriptional gene silencing<br />
<br />
=== mRNA degradation ===<br />
<br />
Figure 2l, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: lncRNAs modulate mRNA stability by associating with proteins involved in mRNA degradation. Left, double-stranded RNAs formed by Alu-containing lncRNAs with mRNA 3′ UTRs recruit STAU1 to induce STAU1-mediated mRNA decay (SMD). Right, NORAD stabilizes PUMILIO 1/2 (PUM1/2)-targeted mRNAs via sequestering PUM1/2 from mRNAs.<br />
<br />
LncRNA (NORAD) annotations:<br />
* MF: GO:1903231 mRNA base-pairing translational repressor activity + additional information (eg part_of GO:0000512 lncRNA-mediated post-transcriptional gene silencing)<br />
* BP: GO:0000512 lncRNA-mediated post-transcriptional gene silencing<br />
<br />
=== mRNA translation repression ===<br />
<br />
Figure 2m, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: lncRNAs regulate translation. Association of lincRNA-p21 (linc-p21) with HuR favours the recruitment of let-7/Ago2, leading to its destabilization. In the absence of HuR, lincRNA-p21 identifies mRNA targets to repress their translation by recruiting the translation repressor Rck129. RISC, RNA-induced silencing complex.<br />
<br />
LncRNA annotations:<br />
* MF: GO:1903231 mRNA base-pairing translational repressor activity + additional information (eg part_of GO:0000512 lncRNA-mediated post-transcriptional gene silencing)<br />
* BP: GO:0000512 lncRNA-mediated post-transcriptional gene silencing<br />
<br />
=== regulation of post-translational modifications ===<br />
<br />
Figure 2n, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: lncRNAs modulate post-translational modifications. Lnc-DC directly interacts with STAT3 to prevent its dephosphorylation by SHP1 (PTPN6).<br />
(From PMID:31857450: Phosphorylated STAT3 translocates in to the nucleus and activates transcription involved in dendritic cell differentiation)<br />
<br />
LncRNA annotations:URS00007B42BD_9606 (lnc-DC; HSALNT0243356) from PMID:31857450 'The STAT3-binding long noncoding RNA lnc-DC controls human dendritic cell differentiation'<br />
* MF: GO:0019212 phosphatase inhibitor activity<br />
**has_input UniProtKB:P29350 (PTPN6)<br />
* MF: GO:0097677 STAT family protein binding<br />
**has_input UniProtKB:P40763 (STAT3)<br />
<br />
BP terms to describe regulation of pathway and involvement in processes:<br />
* BP: GO:0046427 positive regulation of receptor signaling pathway via JAK-STAT<br />
**BP: GO0097028 dendritic cell differentiation<br />
<br />
<br />
[[Category:Annotation Guidelines]]</div>Hla28https://wiki.geneontology.org/index.php?title=Annotation_Conf._Call_2024-01-30&diff=86505Annotation Conf. Call 2024-01-302024-01-30T16:11:14Z<p>Hla28: /* Attendees */</p>
<hr />
<div>= Agenda and Minutes =<br />
<br />
== Meetings and Announcements ==<br />
<br />
=== Noctua ===<br />
* Next regularly scheduled Noctua outage:<br />
** Thursday, February 8th, 4-6pm PST<br />
*** [https://github.com/geneontology/noctua/issues/857 Outage tasks]<br />
<br />
== GO Release Pipeline ==<br />
* January release on the 17th<br />
* #release-pipeline Slack channel for updates<br />
<br />
== Annotation ==<br />
=== Updating 'has input' and 'has output' extension relations to 'has primary input' and 'has primary output' ===<br />
* RO has relations to distinguish between different types of inputs and outputs to BPs and MFs<br />
* In GO annotation, we generally want to capture just the primary inputs and outputs, i.e. the entity whose transformation is the main goal of the process or function.<br />
** For example, the protein that is a substrate of a kinase or the main chemical that is modified during a metabolic process.<br />
* The GO ontology has already been updated to reflect this.<br />
* Protein2GO will need to be updated.<br />
* Noctua will need to be updated.<br />
<br />
=== ECO codes ===<br />
* Do any groups use more granular ECO codes than the traditional three-letter codes for manual annotation?<br />
<br />
=== Automatic replacements for 'x signaling involved in y' BPs ===<br />
* Replace annotations with 'x signaling' and an annotation extension of part_of 'y'<br />
* Request from Ruth (seems like the table below illustrates what she would like): <br />
** Please could I just say that when I have been revising the of 'x signaling involved in y' BP annotations it has been very helpful to be able to see the parent terms for each term so that I can see what parent annotations to create and what to add to the AE field. So although I have got a lot of these to do I would really appreciate being given a list of the annotations to revise before these are all obsoleted. Or perhaps it would be easier to provide a list of the terms plus their parent terms, so that I can look these up.<br />
* Feedback from Antonia and Malcolm:<br />
** Annotations should be made directly to both the signaling term and the 'involved in' term; the latter shouldn't just be an extension on the signaling term<br />
** In Noctua, even when curators update the annotation to the signaling term plus a 'part of' extension, as long as the original term exists in the ontology, the reasoner will also create an annotation to the compound term<br />
<br />
<br />
[[File:Precomposed_term_replacement.png|1100px]]<br />
<br />
== GO-CAM and Noctua ==<br />
* Update on new standard annotation UI:<br />
** Tremayne has prototype - now on noctua-dev<br />
** Jim is working on rules for adding metadata to all existing Noctua 'models' that would distinguish those that are fully standard annotation 'compliant' from those that have one or more annotations that are not, e.g. include what would be the equivalent of a nested annotation extension or what would be considered a causal model<br />
** Why do we want this? We want to give curators information on what 'models' can be fully manipulated in a table/form interface vs those models that should be manipulated in the VPE or graph editor<br />
<br />
== Ontology ==<br />
<br />
=== Ongoing Projects ===<br />
==== Signaling ====<br />
* [https://github.com/geneontology/go-ontology/issues/26899 Merge GO:0019933 cAMP-mediated signaling & regulation children GO:0010737 protein kinase A signaling & regulation children]<br />
<br />
== Attendees ==<br />
*On call: Antonia, Colin, Deborah, Dmitry, Dustin, Edith, Giulia, Helen, Kimberly, Leonore, Li, Malcolm, Pascale, Patrick, Raymond, Rob, Rossana, Seth, Sridhar, Stan, Steven, Suzi, Val<br />
<br />
[[Category:Annotation Working Group]]</div>Hla28https://wiki.geneontology.org/index.php?title=LncRNA_GO_annotation_manual&diff=85887LncRNA GO annotation manual2023-09-06T15:19:50Z<p>Hla28: /* molecular condensate scaffold activity */</p>
<hr />
<div>LncRNAs have multiple and varied activities (see [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]] which describes 13 roles of lncRNAs), these guidelines are suggestions for the curation of some of these lncRNAs. These were discussed [https://github.com/geneontology/go-ontology/issues/23028 here].<br />
<br />
===Decision tree to assist with curation of lncRNA:miRNA interactions===<br />
<br />
These guidelines are for the curation of lncRNAs that bind to miRNA and prevent miRNA activity. These lncRNAs are often described as sponge lncRNAs.<br />
<br />
Link to LncRNA_Decision_Tree pdf[[https://wiki.geneontology.org/images/e/e4/LncRNA_Decision_Tree.pdf]]<br />
<br />
[[File:LncRNA Decision Tree.jpg|960x540px]]<br />
<br />
'''Decision Tree for the GO terms and annotation extensions used for capturing targets of lncRNAs.''' The types of evidence in the blue boxes are described further in the text. Information about the cell or tissue that the interaction occurs in can be captured for example in the annotation extension field using: occurs_in (insert cell ontology ID and/or UBERON ID based on cell and/or tissue type respectively). This information can be included when inhibition of the lncRNA leads to an increase in the endogenous miRNA (or decrease in the miRNA target protein level). Slightly weaker evidence to support inclusion of the cell or tissue information would be evidence that the lncRNA is expressed in these cells/this tissue AND that the authors are confident that the lncRNA target is also being regulated in these cells/this tissue. For example, when the addition of the lncRNA leads to a decrease in the endogenous miRNA or increase in the endogenous protein level.<br />
<br />
'''Note:''' to be able to indicate any target in a GO annotation, the prediction evidence does not need to be in the paper you are annotating, it could be from another paper or a prediction database. When looking at predictions or validations in a prediction database, it is recommended to check the references cited for the target as they may serve as a good source of experimental annotation. Additionally, it has been found that some of the cited papers do not support the validation of the targets. Annotations to “miRNA inhibitor activity via base pairing” (GO:0140869) should ONLY be made from the paper containing the experimental evidence, however it is acceptable to indicate in the annotation extension of a “gene silencing by miRNA” annotation that the target of gene silencing is direct (by using ''has_input'') if the evidence for binding is in another paper.<br />
<br />
===Inactivation of X chromosome by heterochromatin formation===<br />
<br />
Figure 2b [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: Xist modulates inactive X chromosome (Xi) architecture during X chromosome inactivation (XCI) by recruiting Xi to associate with the lamin B receptor (LBR) at the nuclear lamina to silence transcription.<br />
<br />
LncRNA (Xist) Annotations:<br />
* MF: GO:0140463 chromatin-protein adaptor activity + appropriate information etc (eg part_of GO:0060820 inactivation of X chromosome by heterochromatin formation)<br />
* BF: GO:0060820 inactivation of X chromosome by heterochromatin formation<br />
<br />
=== DNA-DNA tethering activity ===<br />
<br />
Figure 2c [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: Firre transcripts localize to their transcription site and five additional autosomal chromosomal loci in trans to affect interactions between distant genomic regions.<br />
<br />
LncRNA (Firre) annotations:<br />
* MF: GO:0106260 DNA-DNA tethering activity + appropriate information etc (eg part_of GO:0006325 chromatin organization)<br />
* BP: GO:0006325 chromatin organization<br />
<br />
=== Promoter-enhancer loop anchoring activity ===<br />
<br />
Figure 2d [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: CCAT1-L accumulates in cis to modulate chromatin loops between enhancers and the promoter of MYC.<br />
<br />
LncRNA (CCAT1-L) annotations:<br />
* MF: GO:0140585 promoter-enhancer loop anchoring activity + appropriate information etc (eg part_of GO:0140588 chromatin looping)<br />
* BP: GO:0140588 chromatin looping<br />
<br />
=== Regulation of chromatin accessibility ===<br />
<br />
Figure 2e [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: lncRNAs regulate chromatin accessibility. Left, Xist recruits HDAC1-associated repressor protein (SHARP), silencing the mediator for retinoid and thyroid hormone receptor (SMART) and HDAC3 to silence Xi. Right, Mhrt prevents SWI/SNF binding to corresponding DNA loci.<br />
<br />
LncRNA (Xist) annotations:<br />
* MF: GO:0030674 protein-macromolecule adaptor activity + appropriate information (eg part_of GO:0006338 chromatin remodeling)<br />
* BP: GO:0006338 chromatin remodeling<br />
<br />
LncRNA (Mhrt) annotations based on [[https://pubmed.ncbi.nlm.nih.gov/25119045/ PMID:25119045]]:<br />
* MF: GO:0140311 protein sequestering activity + appropriate information etc (eg has_inputs Brg1/Smarca4, Q3TKT4), part_of GO:0006338 chromatin remodeling)<br />
* BP: GO:0006338 chromatin remodeling<br />
<br />
=== Triplex-Mediated Changes in Chromatin Structure ===<br />
<br />
Figure 2f, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: Khps1 enhances Pol II transcription by forming an R-loop that anchors Khps1-interacting p300/CBP to the SPHK1 promoter.<br />
<br />
LncRNA (Khps1) annotations based on [[https://pubmed.ncbi.nlm.nih.gov/26590717/ PMID: 26590717]]:<br />
<br />
* MF: GO:0030674 protein-macromolecule adaptor activity or GO:0001010 RNA polymerase II sequence-specific DNA-binding transcription factor recruiting activity + appropriate information etc (eg part_of GO:0045944 positive regulation of transcription by RNA polymerase II)<br />
* MF: GO:1990837 sequence-specific double-stranded DNA binding + appropriate information etc (eg part_of GO:0006325 chromatin organization)<br />
* BP: GO:0006325 chromatin organization<br />
* BP: GO:0045944 positive regulation of transcription by RNA polymerase II<br />
<br />
=== RNA polymerase inhibitor activity ===<br />
<br />
Figure 2g, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]:lncRNAs interfere with Pol II transcription machineries both at the initiation (left) and elongation (right) stages.<br />
<br />
LncRNA annotations:<br />
* MF: GO:0140870 RNA polymerase inhibitor activity<br />
* BP:GO:0000122 negative regulation of transcription by RNA polymerase II<br />
<br />
=== repressor of RNA polymerase inhibitor activity ===<br />
<br />
Figure 2h, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: SLERT promotes Pol I transcription by binding DDX21 to alter its conformation, thereby releasing its inhibitory effect on Pol I.<br />
<br />
LncRNA (SLERT) annotations:<br />
* MF: GO:0140871 repressor of RNA polymerase inhibitor activity + appropriate information (eg has_input DDX21)<br />
* BP: GO:0045943 positive regulation of transcription by RNA polymerase I<br />
<br />
=== molecular condensate scaffold activity ===<br />
<br />
Figure 2i, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: NEAT1 is an architectural lncRNA that nucleates paraspeckles. Upon cellular stress, altered NEAT1 transcription and processing lead to changes of paraspeckles. PSP, paraspeckle proteins.<br />
<br />
LncRNA (NEAT1) annotations:<br />
* MF: GO:0140693 molecular condensate scaffold activity + additional information (eg part_of GO:0006325 chromatin organization or GO:0006996 organelle organization)<br />
* BP: GO:0030575 nuclear body organization<br />
<br />
=== miRNA inhibitor activity / sponge ===<br />
<br />
See decision tree above <br />
Figure 2k, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: A regulatory network consisting of different types of ncRNAs. Cyrano, harbouring miR-7 binding sites, targets miR-7 for degradation and prevents miR-7 from repressing its target RNAs including the circRNA Cdr1as.<br />
<br />
LncRNA (Cyrano) annotations: <br />
* MF GO:0140869 miRNA inhibitor activity via base-pairing + additional information (eg has_input miR-7 RNAcentral ID, part_of GO:0000512 lncRNA-mediated post-transcriptional gene silencing)<br />
* BP: GO:0000512 lncRNA-mediated post-transcriptional gene silencing<br />
<br />
=== mRNA degradation ===<br />
<br />
Figure 2l, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: lncRNAs modulate mRNA stability by associating with proteins involved in mRNA degradation. Left, double-stranded RNAs formed by Alu-containing lncRNAs with mRNA 3′ UTRs recruit STAU1 to induce STAU1-mediated mRNA decay (SMD). Right, NORAD stabilizes PUMILIO 1/2 (PUM1/2)-targeted mRNAs via sequestering PUM1/2 from mRNAs.<br />
<br />
LncRNA (NORAD) annotations:<br />
* MF: GO:1903231 mRNA base-pairing translational repressor activity + additional information (eg part_of GO:0000512 lncRNA-mediated post-transcriptional gene silencing)<br />
* BP: GO:0000512 lncRNA-mediated post-transcriptional gene silencing<br />
<br />
=== mRNA translation repression ===<br />
<br />
Figure 2m, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: lncRNAs regulate translation. Association of lincRNA-p21 (linc-p21) with HuR favours the recruitment of let-7/Ago2, leading to its destabilization. In the absence of HuR, lincRNA-p21 identifies mRNA targets to repress their translation by recruiting the translation repressor Rck129. RISC, RNA-induced silencing complex.<br />
<br />
LncRNA annotations:<br />
* MF: GO:1903231 mRNA base-pairing translational repressor activity + additional information (eg part_of GO:0000512 lncRNA-mediated post-transcriptional gene silencing)<br />
* BP: GO:0000512 lncRNA-mediated post-transcriptional gene silencing<br />
<br />
=== regulation of post-translational modifications ===<br />
<br />
Figure 2n, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: lncRNAs modulate post-translational modifications. Lnc-DC directly interacts with STAT3 to prevent its dephosphorylation by SHP1.<br />
<br />
LncRNA annotations:<br />
* MF: GO:0019212 phosphatase inhibitor activity and/or GO:0140311 protein sequestering activity<br />
* BP: may be able to associated a GO terms describing the regulation of signaling pathway or other process<br />
<br />
[[Category:Annotation Guidelines]]</div>Hla28https://wiki.geneontology.org/index.php?title=LncRNA_GO_annotation_manual&diff=85886LncRNA GO annotation manual2023-09-06T15:17:29Z<p>Hla28: /* molecular condensate scaffold activity */</p>
<hr />
<div>LncRNAs have multiple and varied activities (see [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]] which describes 13 roles of lncRNAs), these guidelines are suggestions for the curation of some of these lncRNAs. These were discussed [https://github.com/geneontology/go-ontology/issues/23028 here].<br />
<br />
===Decision tree to assist with curation of lncRNA:miRNA interactions===<br />
<br />
These guidelines are for the curation of lncRNAs that bind to miRNA and prevent miRNA activity. These lncRNAs are often described as sponge lncRNAs.<br />
<br />
Link to LncRNA_Decision_Tree pdf[[https://wiki.geneontology.org/images/e/e4/LncRNA_Decision_Tree.pdf]]<br />
<br />
[[File:LncRNA Decision Tree.jpg|960x540px]]<br />
<br />
'''Decision Tree for the GO terms and annotation extensions used for capturing targets of lncRNAs.''' The types of evidence in the blue boxes are described further in the text. Information about the cell or tissue that the interaction occurs in can be captured for example in the annotation extension field using: occurs_in (insert cell ontology ID and/or UBERON ID based on cell and/or tissue type respectively). This information can be included when inhibition of the lncRNA leads to an increase in the endogenous miRNA (or decrease in the miRNA target protein level). Slightly weaker evidence to support inclusion of the cell or tissue information would be evidence that the lncRNA is expressed in these cells/this tissue AND that the authors are confident that the lncRNA target is also being regulated in these cells/this tissue. For example, when the addition of the lncRNA leads to a decrease in the endogenous miRNA or increase in the endogenous protein level.<br />
<br />
'''Note:''' to be able to indicate any target in a GO annotation, the prediction evidence does not need to be in the paper you are annotating, it could be from another paper or a prediction database. When looking at predictions or validations in a prediction database, it is recommended to check the references cited for the target as they may serve as a good source of experimental annotation. Additionally, it has been found that some of the cited papers do not support the validation of the targets. Annotations to “miRNA inhibitor activity via base pairing” (GO:0140869) should ONLY be made from the paper containing the experimental evidence, however it is acceptable to indicate in the annotation extension of a “gene silencing by miRNA” annotation that the target of gene silencing is direct (by using ''has_input'') if the evidence for binding is in another paper.<br />
<br />
===Inactivation of X chromosome by heterochromatin formation===<br />
<br />
Figure 2b [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: Xist modulates inactive X chromosome (Xi) architecture during X chromosome inactivation (XCI) by recruiting Xi to associate with the lamin B receptor (LBR) at the nuclear lamina to silence transcription.<br />
<br />
LncRNA (Xist) Annotations:<br />
* MF: GO:0140463 chromatin-protein adaptor activity + appropriate information etc (eg part_of GO:0060820 inactivation of X chromosome by heterochromatin formation)<br />
* BF: GO:0060820 inactivation of X chromosome by heterochromatin formation<br />
<br />
=== DNA-DNA tethering activity ===<br />
<br />
Figure 2c [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: Firre transcripts localize to their transcription site and five additional autosomal chromosomal loci in trans to affect interactions between distant genomic regions.<br />
<br />
LncRNA (Firre) annotations:<br />
* MF: GO:0106260 DNA-DNA tethering activity + appropriate information etc (eg part_of GO:0006325 chromatin organization)<br />
* BP: GO:0006325 chromatin organization<br />
<br />
=== Promoter-enhancer loop anchoring activity ===<br />
<br />
Figure 2d [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: CCAT1-L accumulates in cis to modulate chromatin loops between enhancers and the promoter of MYC.<br />
<br />
LncRNA (CCAT1-L) annotations:<br />
* MF: GO:0140585 promoter-enhancer loop anchoring activity + appropriate information etc (eg part_of GO:0140588 chromatin looping)<br />
* BP: GO:0140588 chromatin looping<br />
<br />
=== Regulation of chromatin accessibility ===<br />
<br />
Figure 2e [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: lncRNAs regulate chromatin accessibility. Left, Xist recruits HDAC1-associated repressor protein (SHARP), silencing the mediator for retinoid and thyroid hormone receptor (SMART) and HDAC3 to silence Xi. Right, Mhrt prevents SWI/SNF binding to corresponding DNA loci.<br />
<br />
LncRNA (Xist) annotations:<br />
* MF: GO:0030674 protein-macromolecule adaptor activity + appropriate information (eg part_of GO:0006338 chromatin remodeling)<br />
* BP: GO:0006338 chromatin remodeling<br />
<br />
LncRNA (Mhrt) annotations based on [[https://pubmed.ncbi.nlm.nih.gov/25119045/ PMID:25119045]]:<br />
* MF: GO:0140311 protein sequestering activity + appropriate information etc (eg has_inputs Brg1/Smarca4, Q3TKT4), part_of GO:0006338 chromatin remodeling)<br />
* BP: GO:0006338 chromatin remodeling<br />
<br />
=== Triplex-Mediated Changes in Chromatin Structure ===<br />
<br />
Figure 2f, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: Khps1 enhances Pol II transcription by forming an R-loop that anchors Khps1-interacting p300/CBP to the SPHK1 promoter.<br />
<br />
LncRNA (Khps1) annotations based on [[https://pubmed.ncbi.nlm.nih.gov/26590717/ PMID: 26590717]]:<br />
<br />
* MF: GO:0030674 protein-macromolecule adaptor activity or GO:0001010 RNA polymerase II sequence-specific DNA-binding transcription factor recruiting activity + appropriate information etc (eg part_of GO:0045944 positive regulation of transcription by RNA polymerase II)<br />
* MF: GO:1990837 sequence-specific double-stranded DNA binding + appropriate information etc (eg part_of GO:0006325 chromatin organization)<br />
* BP: GO:0006325 chromatin organization<br />
* BP: GO:0045944 positive regulation of transcription by RNA polymerase II<br />
<br />
=== RNA polymerase inhibitor activity ===<br />
<br />
Figure 2g, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]:lncRNAs interfere with Pol II transcription machineries both at the initiation (left) and elongation (right) stages.<br />
<br />
LncRNA annotations:<br />
* MF: GO:0140870 RNA polymerase inhibitor activity<br />
* BP:GO:0000122 negative regulation of transcription by RNA polymerase II<br />
<br />
=== repressor of RNA polymerase inhibitor activity ===<br />
<br />
Figure 2h, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: SLERT promotes Pol I transcription by binding DDX21 to alter its conformation, thereby releasing its inhibitory effect on Pol I.<br />
<br />
LncRNA (SLERT) annotations:<br />
* MF: GO:0140871 repressor of RNA polymerase inhibitor activity + appropriate information (eg has_input DDX21)<br />
* BP: GO:0045943 positive regulation of transcription by RNA polymerase I<br />
<br />
=== molecular condensate scaffold activity ===<br />
<br />
Figure 2i, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: NEAT1 is an architectural lncRNA that nucleates paraspeckles. Upon cellular stress, altered NEAT1 transcription and processing lead to changes of paraspeckles. PSP, paraspeckle proteins.<br />
<br />
LncRNA (NEAT1) annotations:<br />
* MF: GO:0140693 molecular condensate scaffold activity + additional information (eg part_of GO:0006325 chromatin organization)<br />
* BP: GO:0030575 nuclear body organization<br />
<br />
=== miRNA inhibitor activity / sponge ===<br />
<br />
See decision tree above <br />
Figure 2k, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: A regulatory network consisting of different types of ncRNAs. Cyrano, harbouring miR-7 binding sites, targets miR-7 for degradation and prevents miR-7 from repressing its target RNAs including the circRNA Cdr1as.<br />
<br />
LncRNA (Cyrano) annotations: <br />
* MF GO:0140869 miRNA inhibitor activity via base-pairing + additional information (eg has_input miR-7 RNAcentral ID, part_of GO:0000512 lncRNA-mediated post-transcriptional gene silencing)<br />
* BP: GO:0000512 lncRNA-mediated post-transcriptional gene silencing<br />
<br />
=== mRNA degradation ===<br />
<br />
Figure 2l, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: lncRNAs modulate mRNA stability by associating with proteins involved in mRNA degradation. Left, double-stranded RNAs formed by Alu-containing lncRNAs with mRNA 3′ UTRs recruit STAU1 to induce STAU1-mediated mRNA decay (SMD). Right, NORAD stabilizes PUMILIO 1/2 (PUM1/2)-targeted mRNAs via sequestering PUM1/2 from mRNAs.<br />
<br />
LncRNA (NORAD) annotations:<br />
* MF: GO:1903231 mRNA base-pairing translational repressor activity + additional information (eg part_of GO:0000512 lncRNA-mediated post-transcriptional gene silencing)<br />
* BP: GO:0000512 lncRNA-mediated post-transcriptional gene silencing<br />
<br />
=== mRNA translation repression ===<br />
<br />
Figure 2m, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: lncRNAs regulate translation. Association of lincRNA-p21 (linc-p21) with HuR favours the recruitment of let-7/Ago2, leading to its destabilization. In the absence of HuR, lincRNA-p21 identifies mRNA targets to repress their translation by recruiting the translation repressor Rck129. RISC, RNA-induced silencing complex.<br />
<br />
LncRNA annotations:<br />
* MF: GO:1903231 mRNA base-pairing translational repressor activity + additional information (eg part_of GO:0000512 lncRNA-mediated post-transcriptional gene silencing)<br />
* BP: GO:0000512 lncRNA-mediated post-transcriptional gene silencing<br />
<br />
=== regulation of post-translational modifications ===<br />
<br />
Figure 2n, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: lncRNAs modulate post-translational modifications. Lnc-DC directly interacts with STAT3 to prevent its dephosphorylation by SHP1.<br />
<br />
LncRNA annotations:<br />
* MF: GO:0019212 phosphatase inhibitor activity and/or GO:0140311 protein sequestering activity<br />
* BP: may be able to associated a GO terms describing the regulation of signaling pathway or other process<br />
<br />
[[Category:Annotation Guidelines]]</div>Hla28https://wiki.geneontology.org/index.php?title=LncRNA_GO_annotation_manual&diff=85739LncRNA GO annotation manual2023-07-28T12:41:07Z<p>Hla28: /* repressor of RNA polymerase inhibitor activity */</p>
<hr />
<div>LncRNAs have multiple and varied activities (see [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]] which describes 13 roles of lncRNAs), these guidelines are suggestions for the curation of some of these lncRNAs. These were discussed [https://github.com/geneontology/go-ontology/issues/23028 here].<br />
<br />
===Decision tree to assist with curation of lncRNA:miRNA interactions===<br />
<br />
These guidelines are for the curation of lncRNAs that bind to miRNA and prevent miRNA activity. These lncRNAs are often described as sponge lncRNAs.<br />
<br />
Link to LncRNA_Decision_Tree pdf[[https://wiki.geneontology.org/images/e/e4/LncRNA_Decision_Tree.pdf]]<br />
<br />
[[File:LncRNA Decision Tree.jpg|960x540px]]<br />
<br />
'''Decision Tree for the GO terms and annotation extensions used for capturing targets of lncRNAs.''' The types of evidence in the blue boxes are described further in the text. Information about the cell or tissue that the interaction occurs in can be captured for example in the annotation extension field using: occurs_in (insert cell ontology ID and/or UBERON ID based on cell and/or tissue type respectively). This information can be included when inhibition of the lncRNA leads to an increase in the endogenous miRNA (or decrease in the miRNA target protein level). Slightly weaker evidence to support inclusion of the cell or tissue information would be evidence that the lncRNA is expressed in these cells/this tissue AND that the authors are confident that the lncRNA target is also being regulated in these cells/this tissue. For example, when the addition of the lncRNA leads to a decrease in the endogenous miRNA or increase in the endogenous protein level.<br />
<br />
'''Note:''' to be able to indicate any target in a GO annotation, the prediction evidence does not need to be in the paper you are annotating, it could be from another paper or a prediction database. When looking at predictions or validations in a prediction database, it is recommended to check the references cited for the target as they may serve as a good source of experimental annotation. Additionally, it has been found that some of the cited papers do not support the validation of the targets. Annotations to “miRNA inhibitor activity via base pairing” (GO:0140869) should ONLY be made from the paper containing the experimental evidence, however it is acceptable to indicate in the annotation extension of a “gene silencing by miRNA” annotation that the target of gene silencing is direct (by using ''has_input'') if the evidence for binding is in another paper.<br />
<br />
===Inactivation of X chromosome by heterochromatin formation===<br />
<br />
Figure 2b [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: Xist modulates inactive X chromosome (Xi) architecture during X chromosome inactivation (XCI) by recruiting Xi to associate with the lamin B receptor (LBR) at the nuclear lamina to silence transcription.<br />
<br />
LncRNA (Xist) Annotations:<br />
* MF: GO:0140463 chromatin-protein adaptor activity + appropriate information etc (eg part_of GO:0060820 inactivation of X chromosome by heterochromatin formation)<br />
* BF: GO:0060820 inactivation of X chromosome by heterochromatin formation<br />
<br />
=== DNA-DNA tethering activity ===<br />
<br />
Figure 2c [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: Firre transcripts localize to their transcription site and five additional autosomal chromosomal loci in trans to affect interactions between distant genomic regions.<br />
<br />
LncRNA (Firre) annotations:<br />
* MF: GO:0106260 DNA-DNA tethering activity + appropriate information etc (eg part_of GO:0006325 chromatin organization)<br />
* BP: GO:0006325 chromatin organization<br />
<br />
=== Promoter-enhancer loop anchoring activity ===<br />
<br />
Figure 2d [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: CCAT1-L accumulates in cis to modulate chromatin loops between enhancers and the promoter of MYC.<br />
<br />
LncRNA (CCAT1-L) annotations:<br />
* MF: GO:0140585 promoter-enhancer loop anchoring activity + appropriate information etc (eg part_of GO:0140588 chromatin looping)<br />
* BP: GO:0140588 chromatin looping<br />
<br />
=== Regulation of chromatin accessibility ===<br />
<br />
Figure 2e [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: lncRNAs regulate chromatin accessibility. Left, Xist recruits HDAC1-associated repressor protein (SHARP), silencing the mediator for retinoid and thyroid hormone receptor (SMART) and HDAC3 to silence Xi. Right, Mhrt prevents SWI/SNF binding to corresponding DNA loci.<br />
<br />
LncRNA (Xist) annotations:<br />
* MF: GO:0030674 protein-macromolecule adaptor activity + appropriate information (eg part_of GO:0006338 chromatin remodeling)<br />
* BP: GO:0006338 chromatin remodeling<br />
<br />
LncRNA (Mhrt) annotations based on [[https://pubmed.ncbi.nlm.nih.gov/25119045/ PMID:25119045]]:<br />
* MF: GO:0140311 protein sequestering activity + appropriate information etc (eg has_inputs Brg1/Smarca4, Q3TKT4), part_of GO:0006338 chromatin remodeling)<br />
* BP: GO:0006338 chromatin remodeling<br />
<br />
=== Triplex-Mediated Changes in Chromatin Structure ===<br />
<br />
Figure 2f, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: Khps1 enhances Pol II transcription by forming an R-loop that anchors Khps1-interacting p300/CBP to the SPHK1 promoter.<br />
<br />
LncRNA (Khps1) annotations based on [[https://pubmed.ncbi.nlm.nih.gov/26590717/ PMID: 26590717]]:<br />
<br />
* MF: GO:0030674 protein-macromolecule adaptor activity or GO:0001010 RNA polymerase II sequence-specific DNA-binding transcription factor recruiting activity + appropriate information etc (eg part_of GO:0045944 positive regulation of transcription by RNA polymerase II)<br />
* MF: GO:1990837 sequence-specific double-stranded DNA binding + appropriate information etc (eg part_of GO:0006325 chromatin organization)<br />
* BP: GO:0006325 chromatin organization<br />
* BP: GO:0045944 positive regulation of transcription by RNA polymerase II<br />
<br />
=== RNA polymerase inhibitor activity ===<br />
<br />
Figure 2g, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]:lncRNAs interfere with Pol II transcription machineries both at the initiation (left) and elongation (right) stages.<br />
<br />
LncRNA annotations:<br />
* MF: GO:0140870 RNA polymerase inhibitor activity<br />
* BP:GO:0000122 negative regulation of transcription by RNA polymerase II<br />
<br />
=== repressor of RNA polymerase inhibitor activity ===<br />
<br />
Figure 2h, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: SLERT promotes Pol I transcription by binding DDX21 to alter its conformation, thereby releasing its inhibitory effect on Pol I.<br />
<br />
LncRNA (SLERT) annotations:<br />
* MF: GO:0140871 repressor of RNA polymerase inhibitor activity + appropriate information (eg has_input DDX21)<br />
* BP: GO:0045943 positive regulation of transcription by RNA polymerase I<br />
<br />
=== molecular condensate scaffold activity ===<br />
<br />
Figure 2i, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: NEAT1 is an architectural lncRNA that nucleates paraspeckles. Upon cellular stress, altered NEAT1 transcription and processing lead to changes of paraspeckles. PSP, paraspeckle proteins.<br />
<br />
LncRNA (NEAT1) annotations:<br />
* MF: GO:0140693 molecular condensate scaffold activity + additional information (eg part_of GO:0006325 chromatin organization)<br />
* BP: GO:0006325 chromatin organization<br />
<br />
=== miRNA inhibitor activity / sponge ===<br />
<br />
See decision tree above <br />
Figure 2k, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: A regulatory network consisting of different types of ncRNAs. Cyrano, harbouring miR-7 binding sites, targets miR-7 for degradation and prevents miR-7 from repressing its target RNAs including the circRNA Cdr1as.<br />
<br />
LncRNA (Cyrano) annotations: <br />
* MF GO:0140869 miRNA inhibitor activity via base-pairing + additional information (eg has_input miR-7 RNAcentral ID, part_of GO:0000512 lncRNA-mediated post-transcriptional gene silencing)<br />
* BP: GO:0000512 lncRNA-mediated post-transcriptional gene silencing<br />
<br />
=== mRNA degradation ===<br />
<br />
Figure 2l, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: lncRNAs modulate mRNA stability by associating with proteins involved in mRNA degradation. Left, double-stranded RNAs formed by Alu-containing lncRNAs with mRNA 3′ UTRs recruit STAU1 to induce STAU1-mediated mRNA decay (SMD). Right, NORAD stabilizes PUMILIO 1/2 (PUM1/2)-targeted mRNAs via sequestering PUM1/2 from mRNAs.<br />
<br />
LncRNA (NORAD) annotations:<br />
* MF: GO:1903231 mRNA base-pairing translational repressor activity + additional information (eg part_of GO:0000512 lncRNA-mediated post-transcriptional gene silencing)<br />
* BP: GO:0000512 lncRNA-mediated post-transcriptional gene silencing<br />
<br />
=== mRNA translation repression ===<br />
<br />
Figure 2m, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: lncRNAs regulate translation. Association of lincRNA-p21 (linc-p21) with HuR favours the recruitment of let-7/Ago2, leading to its destabilization. In the absence of HuR, lincRNA-p21 identifies mRNA targets to repress their translation by recruiting the translation repressor Rck129. RISC, RNA-induced silencing complex.<br />
<br />
LncRNA annotations:<br />
* MF: GO:1903231 mRNA base-pairing translational repressor activity + additional information (eg part_of GO:0000512 lncRNA-mediated post-transcriptional gene silencing)<br />
* BP: GO:0000512 lncRNA-mediated post-transcriptional gene silencing<br />
<br />
=== regulation of post-translational modifications ===<br />
<br />
Figure 2n, [[https://pubmed.ncbi.nlm.nih.gov/31048766/ PMID:31048766]]: lncRNAs modulate post-translational modifications. Lnc-DC directly interacts with STAT3 to prevent its dephosphorylation by SHP1.<br />
<br />
LncRNA annotations:<br />
* MF: GO:0019212 phosphatase inhibitor activity and/or GO:0140311 protein sequestering activity<br />
* BP: may be able to associated a GO terms describing the regulation of signaling pathway or other process<br />
<br />
[[Category:Annotation Guidelines]]</div>Hla28https://wiki.geneontology.org/index.php?title=File:MiRNA_Annotation_Decision_Tree_2023.png&diff=85609File:MiRNA Annotation Decision Tree 2023.png2023-07-12T15:38:55Z<p>Hla28: Hla28 uploaded a new version of File:MiRNA Annotation Decision Tree 2023.png</p>
<hr />
<div>Agreed approach for the curation of miRNAs</div>Hla28https://wiki.geneontology.org/index.php?title=File:MiRNA_Annotation_Decision_Tree_2023.png&diff=85608File:MiRNA Annotation Decision Tree 2023.png2023-07-12T15:35:23Z<p>Hla28: Hla28 reverted File:MiRNA Annotation Decision Tree 2023.png to an old version</p>
<hr />
<div>Agreed approach for the curation of miRNAs</div>Hla28https://wiki.geneontology.org/index.php?title=File:MiRNA_Annotation_Decision_Tree_2023.png&diff=85607File:MiRNA Annotation Decision Tree 2023.png2023-07-12T15:32:04Z<p>Hla28: Hla28 uploaded a new version of File:MiRNA Annotation Decision Tree 2023.png</p>
<hr />
<div>Agreed approach for the curation of miRNAs</div>Hla28https://wiki.geneontology.org/index.php?title=Annotation_Conf._Call_2022-06-21&diff=82722Annotation Conf. Call 2022-06-212022-06-21T15:12:46Z<p>Hla28: /* Attendees */</p>
<hr />
<div>= Agenda and Minutes =<br />
<br />
== Meetings and Announcements ==<br />
<br />
=== Fall 2022 Consortium Meeting ===<br />
*Possible in-person meeting; location and dates still TBD<br />
<br />
=== Noctua ===<br />
*Regularly scheduled Noctua outage:<br />
**Thursday, June 23rd<br />
<br />
== GO Release Pipeline ==<br />
* June release<br />
<br />
== AmiGO ==<br />
<br />
== Ontology ==<br />
<br />
=== Membrane CC Terms ===<br />
*Proposal to obsolete and reorganize CC ontology for membrane annotations<br />
** Capturing membrane protein topology will no longer be under the purview of GO annotation<br />
** [https://github.com/geneontology/go-annotation/issues/4187 Review 'integral to membrane protein annotations']<br />
*** [https://docs.google.com/document/d/1xSUmYaBmP0PA9VUAqIYZtHO6pidF-Zk3xqhcoN9p-mo/edit SOP] for examining topology and GO CC annotations in UniProtKB<br />
<br />
===Cell cortex definition===<br />
*https://github.com/geneontology/go-ontology/issues/23429<br />
<br />
== Annotation ==<br />
<br />
=== Review 'has input' and With/From documentation ===<br />
*[https://wiki.geneontology.org/Annotation_Extension_Relation:has_input#Distinction_between_'has_input'_and_'with/from' Current has input and 'with from' documentation]<br />
<br />
=== Annotation error reports and annotation review ===<br />
* Please remember to keep checking the [http://current.geneontology.org/reports/index.html reports] generated by the pipeline and address any errors<br />
* Also check annotation review tickets assigned to you/your group in go-annotation repo on github<br />
* Questions about either - please bring to the meeting<br />
<br />
== GO-CAM and Noctua ==<br />
<br />
== Other Projects ==<br />
<br />
<br />
<br />
== Attendees ==<br />
*On call: David, Debbie, Dustin, Giulia, Harold, Helen, Jodi, Kimberly, Li, Mahima, Malcolm, Mary, Pascale, Patrick, Raymond, Rob, Seth, Suzi <br />
[[Category:Annotation Working Group]]</div>Hla28https://wiki.geneontology.org/index.php?title=Elements_of_an_annotation&diff=82403Elements of an annotation2022-04-28T12:17:24Z<p>Hla28: /* Negation */</p>
<hr />
<div>This page describes the different annotation fields. <br />
<br />
=Elements of an annotation=<br />
==Annotation Subject==<br />
* Annotations subjects consists of valid database identifiers, such as WB:WBGene00003721, SGD:S000001048, or UniProtKB:P99999. <br />
* Annotations subjects may be genes or gene products (e.g. proteins, including specific isoforms; ncRNAs; and protein complexes)<br />
* The list of valid database prefixes can be found on the [http://amigo.geneontology.org/xrefs GO website].<br />
<br />
==Relations==<br />
* Annotation Subjects and GO terms are linked by a '''Relation''' from the [https://github.com/oborel/obo-relations Relations Ontology].<br />
* The relations applicable to each aspect of GO as well as usage guidelines can be found in the [[Annotation_Relations]] page.<br />
<br />
==Negation==<br />
<br />
* The NOT statement indicates that the gene product does not enable a Molecular Function, is not part of a Biological Process or is not located in a specific Cellular Component. <br />
* NOT statements are only used when a user might expect that the gene product would have a specific biological property (MF, BP or CC). <br />
* Contrary to positive annotations, NOT statements propagate ''down'' the ontology, such that the annotation <code>gene product NOT enables protein kinase activity</code> means that the gene product does not enable protein serine/threonine kinase activity or protein tyrosine kinase activity either.<br />
* Both positive and NOT statements can be used in cases where there is conflicting experimental findings in the literature.<br />
* If an isoform has a different function from the main isoform represented by the gene-centric entity, a NOT annotation can be captured together with the isoform identifier.<br />
* NOT annotations can be supported by experiments that show the lack of activity (or BP, CC), or based on sequence data that it has lost essential residues and is unlikely to be able to carry out a function, participate in a process, or be found in a certain location. In this case the evidence code is [http://wiki.geneontology.org/index.php/Inferred_from_Key_Residues_(IKR) IKR (Inferred from Key Residue)] evidence code.<br />
<br />
'''When NOT to use negation'''<br />
* The NOT qualifier should be not used to capture every experimental result. <br />
** For example in a subcellular localization experiment, locations where the gene product is not found should not be captured, unless it is explicitly needed. If a protein is found in the nucleus but not in the mitochondrion, usually a <code>NOT located in mitochondrion</code> annotation would be inappropriate,<br />
* The NOT qualifier should be not used to annotate negative or inconclusive experimental results.<br />
** For example, if a mutant develops a specific anatomical structure, it doesn't imply that it does not contribute to the process; the experiment may just not allow to make the positive conclusion.<br />
* The NOT qualifier should be not used to describe experimental conditions or specific contexts in which the gene product is not active (i.e, should not be used in combination with an extension).<br />
<br />
'''Examples'''<br />
* '''MNN4 (CGD:CAL0000174110) NOT biological process involved in interspecies interaction between organisms''' from PMID:15271989, based on the result that loss of cell wall mannosylphosphate in Candida albicans does not influence macrophage recognition. This NOT annotation means that MNN4 is never involved in any biological process involved in interspecies interaction between organisms, which the data from the paper does not allow to conclude.<br />
<br />
==GO term==<br />
* A gene product can be annotated to zero or more terms from each ontology.<br />
* Guidelines for certain specific topics are in the [[Annotation#Topic-Specific_Guidelines]] section.<br />
<br />
== Annotation Extensions ==<br />
* Annotation extensions may be added to GO annotations to provide additional contextual information for the assertion.<br />
* Annotation extensions are structured text that use a relation from the Relations Ontology and an appropriate biological concept or entity to modify the GO annotation, e.g. nucleus 'part of' epithelial cell.<br />
* Detailed documentation on curation using annotation extensions can be found here: [[Annotation_Extension]]<br />
<br />
==Evidence==<br />
* Each annotation must indicate what kind of evidence supports the association between the gene product and the GO term. <br />
* Annotations use Evidence Codes from the [http://www.evidenceontology.org/ Evidence and Conclusions Ontology]. <br />
* See the [[Guide to GO Evidence Codes]] for details. <br />
<br />
==Reference==<br />
* Every annotation must also cite a reference, which may be either a publication or an internal GO reference (https://github.com/geneontology/go-site/tree/master/metadata/gorefs). <br />
<br />
== Assigned_by ==<br />
Every annotation is marked with the name of the group that made the annotation. <br />
The group that made the annotation may be different from the database who manages the identifiers and/or the annotation file.<br />
<br />
== Date ==<br />
The date the annotation was made or last edited, in YYYYMMDD format.<br />
<br />
== Review Status ==<br />
<br />
Last reviewed: 2022-04-19<br />
<br />
<br />
[[Category: Annotation]]</div>Hla28https://wiki.geneontology.org/index.php?title=Elements_of_an_annotation&diff=82350Elements of an annotation2022-04-19T18:36:01Z<p>Hla28: /* Negation */</p>
<hr />
<div>This page describes the different annotation fields. <br />
<br />
=Elements of an annotation=<br />
==Annotation Subject==<br />
* Annotations subjects consists of valid database identifiers, such as WB:WBGene00003721, SGD:S000001048, or UniProtKB:P99999. <br />
* Annotations subjects may be genes or gene products (e.g. proteins, including specific isoforms; ncRNAs; and protein complexes)<br />
* The list of valid database prefixes can be found on the [http://amigo.geneontology.org/xrefs GO website].<br />
<br />
==Relations==<br />
* Annotation Subjects and GO terms are linked by a '''Relation''' from the [https://github.com/oborel/obo-relations Relations Ontology].<br />
* The relations applicable to each aspect of GO as well as usage guidelines can be found in the [[Annotation_Relations]] page.<br />
<br />
==Negation==<br />
<br />
* The NOT statement indicates that the gene product does not enable a Molecular Function, is not part of a Biological Process or is not located in a specific Cellular Component. <br />
* NOT statements are only used when a user might expect that the gene product would have a specific biological property (MF, BP or CC). <br />
* Contrary to positive annotations, NOT statements propagate ''down'' the ontology. For instance, <code>gene product NOT enables protein kinase activity</code> means that the gene product does not enable protein serine/threonine kinase activity or protein tyrosine kinase activity either.<br />
* Both positive and NOT statements can be used in cases where there is conflicting experimental findings in the literature.<br />
* If an isoform has a different function from the main isoform represented by the gene-centric entity, a NOT annotation can be captured together with the isoform identifier.<br />
* NOT annotations can be supported by experiments that show the lack of activity (or BP, CC), or based on sequence data that it has lost essential residues and is unlikely to be able to carry out a function, participate in a process, or be found in a certain location. In this case the evidence code is [http://wiki.geneontology.org/index.php/Inferred_from_Key_Residues_(IKR) IKR (Inferred from Key Residue)] evidence code.<br />
<br />
'''When NOT to use negation'''<br />
* The NOT qualifier should be not used to capture every experimental result. <br />
** For example in a subcellular localization experiment, locations where the gene product is not found should not be captured, unless it is explicitly needed. If a protein is found in the nucleus but not in the mitochondrion, usually a <code>NOT located in mitochondrion</code> annotation would be inappropriate,<br />
* The NOT qualifier should be not used to annotate negative or inconclusive experimental results.<br />
** For example, if a mutant fails to develop a specific anatomical structure, it doesn't imply that it does not contribute to the process; the experiment may just not allow to make the positive conclusion.<br />
* The NOT qualifier should be not used to describe experimental conditions or specific contexts in which the gene product is not active (i.e, should not be used in combination with an extension).<br />
<br />
==GO term==<br />
* A gene product can be annotated to zero or more terms from each ontology.<br />
* Guidelines for certain specific topics are in the [[Annotation#Topic-Specific_Guidelines]] section.<br />
<br />
== Annotation Extensions ==<br />
* Annotation extensions may be added to GO annotations to provide additional contextual information for the assertion.<br />
* Annotation extensions are structured text that use a relation from the Relations Ontology and an appropriate biological concept or entity to modify the GO annotation, e.g. nucleus 'part of' epithelial cell.<br />
* Detailed documentation on curation using annotation extensions can be found here: [[Annotation_Extension]]<br />
<br />
==Evidence==<br />
* Each annotation must indicate what kind of evidence supports the association between the gene product and the GO term. <br />
* Annotations use Evidence Codes from the [http://www.evidenceontology.org/ Evidence and Conclusions Ontology]. <br />
* See the [[Guide to GO Evidence Codes]] for details. <br />
<br />
==Reference==<br />
* Every annotation must also cite a reference, which may be either a publication or an internal GO reference (https://github.com/geneontology/go-site/tree/master/metadata/gorefs). <br />
<br />
== Assigned_by ==<br />
Every annotation is marked with the name of the group that made the annotation. <br />
The group that made the annotation may be different from the database who manages the identifiers and/or the annotation file.<br />
<br />
== Date ==<br />
The date the annotation was made or last edited, in YYYYMMDD format.<br />
<br />
== Review Status ==<br />
<br />
Last reviewed: 2022-04-19<br />
<br />
<br />
[[Category: Annotation]]</div>Hla28https://wiki.geneontology.org/index.php?title=Elements_of_an_annotation&diff=82349Elements of an annotation2022-04-19T18:34:42Z<p>Hla28: /* Negation */</p>
<hr />
<div>This page describes the different annotation fields. <br />
<br />
=Elements of an annotation=<br />
==Annotation Subject==<br />
* Annotations subjects consists of valid database identifiers, such as WB:WBGene00003721, SGD:S000001048, or UniProtKB:P99999. <br />
* Annotations subjects may be genes or gene products (e.g. proteins, including specific isoforms; ncRNAs; and protein complexes)<br />
* The list of valid database prefixes can be found on the [http://amigo.geneontology.org/xrefs GO website].<br />
<br />
==Relations==<br />
* Annotation Subjects and GO terms are linked by a '''Relation''' from the [https://github.com/oborel/obo-relations Relations Ontology].<br />
* The relations applicable to each aspect of GO as well as usage guidelines can be found in the [[Annotation_Relations]] page.<br />
<br />
==Negation==<br />
<br />
* The NOT statement indicates that the gene product does not enable a Molecular Function, is not part of a Biological Process or is not located in a specific Cellular Component. <br />
* NOT statements are only used when a user might expect that the gene product would have a specific biological property (MF, BP or CC). <br />
* Contrary to positive annotations, NOT statements propagate ''down'' the ontology. For instance, <code>gene product NOT enables protein kinase activity</code> means that the gene product does not enable protein serine/threonine kinase activity or protein tyrosine kinase activity either.<br />
* Both positive and NOT statements can be used in cases where there is conflicting experimental findings in the literature.<br />
* If an isoform has a different function from the main isoform represented by the gene-centric entity, a NOT annotation can be captured together with the isoform identifier.<br />
* NOT annotations can be supported by experiments that show the lack of activity (or BP, CC), or based on sequence data that it has lost essential residues and is unlikely to be able to carry out a function, participate in a process, or be found in a certain location. In this case the evidence code is [http://wiki.geneontology.org/index.php/Inferred_from_Key_Residues_(IKR) IKR (Inferred from Key Residue)] evidence code.<br />
<br />
'''When NOT to use negation'''<br />
* The NOT qualifier should be not used to capture every experimental results. <br />
** For example in a subcellular localization experiment, locations where the gene product is not found should not be captured, unless it is explicitly needed. If a protein is found in the nucleus but not in the mitochondrion, usually a <code>NOT located in mitochondrion</code> annotation would be inappropriate,<br />
* The NOT qualifier should be not used to annotate negative or inconclusive experimental results.<br />
** For example, if a mutant fails to develop a specific anatomical structure, it doesn't imply that it does not contribute to the process; the experiment may just not allow to make the positive conclusion.<br />
* The NOT qualifier should be not used to describe experimental conditions or specific contexts in which the gene product is not active (i.e, should not be used in combination with an extension).<br />
<br />
==GO term==<br />
* A gene product can be annotated to zero or more terms from each ontology.<br />
* Guidelines for certain specific topics are in the [[Annotation#Topic-Specific_Guidelines]] section.<br />
<br />
== Annotation Extensions ==<br />
* Annotation extensions may be added to GO annotations to provide additional contextual information for the assertion.<br />
* Annotation extensions are structured text that use a relation from the Relations Ontology and an appropriate biological concept or entity to modify the GO annotation, e.g. nucleus 'part of' epithelial cell.<br />
* Detailed documentation on curation using annotation extensions can be found here: [[Annotation_Extension]]<br />
<br />
==Evidence==<br />
* Each annotation must indicate what kind of evidence supports the association between the gene product and the GO term. <br />
* Annotations use Evidence Codes from the [http://www.evidenceontology.org/ Evidence and Conclusions Ontology]. <br />
* See the [[Guide to GO Evidence Codes]] for details. <br />
<br />
==Reference==<br />
* Every annotation must also cite a reference, which may be either a publication or an internal GO reference (https://github.com/geneontology/go-site/tree/master/metadata/gorefs). <br />
<br />
== Assigned_by ==<br />
Every annotation is marked with the name of the group that made the annotation. <br />
The group that made the annotation may be different from the database who manages the identifiers and/or the annotation file.<br />
<br />
== Date ==<br />
The date the annotation was made or last edited, in YYYYMMDD format.<br />
<br />
== Review Status ==<br />
<br />
Last reviewed: 2022-04-19<br />
<br />
<br />
[[Category: Annotation]]</div>Hla28https://wiki.geneontology.org/index.php?title=Annotation_Conf._Call_2021-06-29&diff=80447Annotation Conf. Call 2021-06-292021-06-29T15:12:00Z<p>Hla28: /* Attendance */</p>
<hr />
<div>= Agenda and Minutes =<br />
<br />
== Meetings and Announcements ==<br />
<br />
=== October Consortium Meeting ===<br />
* Wednesday, October 13th - Friday, October 15th<br />
* Hosted by:<br />
** University of Maryland Medical School, Baltimore MD<br />
** Michelle Gwinn-Giglio<br />
* [https://docs.google.com/document/d/15_TIWfnu2X_3CVzdcou14PyV4Ff8F9Hz8WSASi1bsaE Agenda]<br />
<br />
=== Noctua Outages ===<br />
* Thursday, July 8th, for ontology/software updates (will now update Noctua every two weeks)<br />
* Saturday, July 10th, (PM PDT) for LBL maintenance<br />
* Will send notification, but please save your work!<br />
<br />
== Annotation Review ==<br />
*[https://github.com/geneontology/go-annotation/issues/3817 Review annotations to GO:0070615 nucleosome-dependent ATPase]<br />
*[https://github.com/geneontology/go-annotation/issues/3819 Review annotations to regulation of motor activity & children]<br />
*[https://github.com/geneontology/go-annotation/issues/3833 Review annotations to GO:0043044 ATP-dependent chromatin remodeling] <br />
*[https://github.com/geneontology/go-annotation/issues/3834 Review annotations to regulation of histone exchange and children]<br />
*Others...<br />
<br />
= Attendance =<br />
* On call: Cailey, David, Dmitry, Giulia, Harold, Kimberly, Malcolm, Pascale, Patrick, Petra, Raymond, Rob, Seth, Suzi, Helen<br />
<br />
[[Category:Annotation Working Group]]</div>Hla28https://wiki.geneontology.org/index.php?title=Contributes_to&diff=79305Contributes to2020-12-15T13:32:03Z<p>Hla28: /* Usage guidance */</p>
<hr />
<div><br />
== Definition ==<br />
A gene product is associated with a GO Molecular Function term using the qualifier 'contributes_to' when it is a member of a complex that is defined as an "irreducible molecular machine" - where a particular Molecular Function cannot be ascribed to an individual subunit or small set of subunits of a complex.<br />
<br />
== Range ==<br />
The 'contributes_to' qualifier can only be used with GO Molecular Function terms.<br />
<br />
== Child Terms ==<br />
None<br />
<br />
==Usage guidance==<br />
* The 'contributes_to' qualifier is used only in cases where a gene product does not perform a molecular function on its own, but as part of an "irreducible molecular machine" where the molecular function cannot be attributed to a subunit or group of subunits. Being part of a complex is not sufficient to use this qualifier. <br />
* In all cases, all intrinsic members of a complex should be annotated to 'part of' some 'GO:0032991 protein-containing complex' or an appropriate child term.<br />
* Checklist: useful questions: <br />
*# Can the activity occur without this subunit? In this case maybe the annotation is not appropriate. <br />
*# Can the protein be annotated to another term? Ideally each protein would have a MF. <br />
*# If the qualifier is omitted, is the annotation still acceptable? (this is to avoid annotating for example regulatory subunits) <br />
<hr><br />
<br />
===Multiple subunits required for a molecular function===<br />
* All subunits of the complex should be assigned the activity using the 'contributes_to' qualifier if the complex can be described as an irreducible molecular machine. <br />
* For example, if a gene product is part of a complex but only has the function as part of that complex, e.g. forms a composite catalytic site that is required for the function, annotate to the molecular function using the qualifier 'contributes_to'. <br />
<br />
'''Examples'''<br />
<br />
1. '''ATP citrate lyase (ACL) in Chlorobaculum tepidum ''': a heterotetrameric enzyme composed of two distinct subunits, with residues from both subunits comprising the active site. Neither of the subunits expressed alone has ACL activity, but co-expression results in ACL activity. Both subunits contribute_to the ATP citrate lyase activity. '''Annotation for ATP citrate lyase subunit 1:'''<br />
Object: UniProt:Q8KDG1 (CT1089) <br />
Relation: contributes_to<br />
GO term: GO:0003878 ATP citrate synthase activity<br />
Evidence code: IDA<br />
PMID:16952946<br />
<br />
<br />
2. '''Subunits of nuclear RNA polymerases:''' none of the individual subunits have RNA polymerase activity, yet all of these subunits contribute_to DNA-dependent RNA polymerase activity. Note that there are gene products that are members of a nuclear RNA polymerase complex that serve other functions besides the polymerase activity. In these cases, the subunits would not be annotated to polymerase activity using the 'contributes to' qualifier. '''Annotation for ''S. pombe'' RNA polymerase II large subunit Rpb1:'''<br />
<br />
Object: SPBC28F2.12<br />
Relation: contributes_to<br />
GO term: GO:0001055 RNA polymerase II activity<br />
Evidence code: EXP<br />
PMID:9325316<br />
<br />
3. '''Subunits of ATP synthase complex ''': The molecular function as described by GO:0046933 'proton-transporting ATP synthase activity, rotational mechanism' cannot be performed by any individual subunit. The proton-transporting membrane sector (F0), the cytoplasmic sector (F1), that catalyzes ATP synthesis by a rotational mechanism, and the stator are required as part of an irreducible molecular machine to perform this function. In this case, all components the ATP synthase complex are annotated to GO:0046933 'proton-transporting ATP synthase activity, rotational mechanism' using the ‘contributes to’ qualifier. '''Annotation for ATP8 ATP synthase complex subunit:'''<br />
Object: SGD:S000007267 (ATP8)<br />
Relation: contributes_to<br />
GO term: GO:0046933 proton-transporting ATP synthase activity, rotational mechanism<br />
Evidence code: IDA<br />
PMID:20691145<br />
<br />
<hr><br />
<br />
===Multi-subunit complex in which the subunit necessary to perform the molecular function is not (yet) known===<br />
<br />
* If a gene product is part of a complex and it is unknown which subunit is responsible for the activity of the complex, do not annotate with a term from the Molecular Function branch of the GO, but use appropriate Cellular Component and Biological Process terms to capture biological knowledge accurately.<br />
<br />
<hr><br />
<br />
===When NOT to use 'contributes_to': single subunit required for a molecular function===<br />
* Being part of a complex does not mean that the molecular function necessarily requires multiple subunits: if a single subunit performs the molecular function, annotate the gene product to this function without any qualifier, but using relation 'enables (Protein2GO) or enabled by (Noctua)'.<br />
* If the gene product forms homomultimers, also annotate the gene product to this function without any qualifier.<br />
<br />
'''Examples'''<br />
Annotate the catalytic subunit, ''without'' the contributes_to qualifier. <br />
<br />
* '''eIF2''': has three subunits (alpha, beta, gamma); one binds GTP; one binds RNA; the whole complex binds the ribosome (all three subunits are required for ribosome binding). So one subunit is annotated to GTP binding and one to RNA binding without qualifiers, and all three stand in the contributes_to relationship to "ribosome binding". The molecular function annotations should have the extension 'occurs_in' eIF2 complex (GO:0005850), and all three are part_of the cellular component eIF2 complex (GO:0005850). <br />
** '''eIF2gamma''' is the actual GTPase, and eIF2alpha and -beta serving accessory functions. Therefore, eIF2gamma is annotated to GTPase activity; the alpha and beta subunits are '''not''' annotated to GTPase activity [https://www.ncbi.nlm.nih.gov/pubmed/29425030]<br />
<br />
* [http://amigo.geneontology.org/amigo/gene_product/UniProtKB:E2RG47 '''STT3'''] [https://www.ncbi.nlm.nih.gov/pubmed/PMID:12887896]: "dolichyl-diphosphooligosaccharide-protein glycotransferase activity": although it is a member of a complex, it is the catalytic subunit, so it should be annotated without the "contributes_to" qualifier.<br />
<br />
*'''PIGM-PIGX complex''': The PIGM-PIGX complex catalyzes GO:0000030 mannosyltransferase activity. PIGM is the sole catalytic subunit, and while the accessory PIGX subunit is required for activity, it does not have the activity [https://www.ncbi.nlm.nih.gov/pubmed/15635094]. <br />
** Therefore, only PIGM is annotated to GO:0000030 mannosyltransferase activity, without 'contributes_to'.<br />
<br />
* '''Prkag1 (protein kinase AMP-activated non-catalytic subunit gamma 1) [http://amigo.geneontology.org/amigo/gene_product/RGD:3388 RGD:3388]''': PMID:21399626 shows that the activation loop of the kinase domain is stabilized by the regulatory domain. The paper also shows that the regulatory subunit binds ADP, so it is really the subunit with a regulatory role. <br />
** annotation should be to "GO:0019887 protein kinase regulator activity"; Prkag1 does NOT contribute to "AMP-activated protein kinase activity".<br />
* '''Prkaa1 (protein kinase AMP-activated catalytic subunit alpha 1) [http://amigo.geneontology.org/amigo/gene_product/RGD:3388 RGD:3387]''' is the active subunit; is should be annotated to "AMP-activated protein kinase activity", without the "contributes_to" qualifier.<br />
<br />
==Specific cases==<br />
Other common functions for protein complex members: <br />
<br />
===Regulatory subunits===<br />
* If a gene product has been identified as the regulatory subunit of a complex, annotate to "X regulator activity" (GO:0098772 molecular function regulator or a child). Use 'has input' some 'gene product' to describe which gene product the annotated gene product regulates.<br />
*Need examples.<br />
<br />
===Adaptor subunits===<br />
* If a gene product is shown to bring together either a subunit of the complex with another protein, a substrate, a membrane, etc., this gene product may be anotated to GO:0060090 molecular adaptor activity or an appropriate child term.<br />
*Need examples.<br />
<br />
== Quality Control Checks ==<br />
<br />
== Relations Ontology ==<br />
[http://www.ontobee.org/ontology/RO?iri=http://purl.obolibrary.org/obo/RO_0002326 contributes to]<br />
<br />
*if and only if exists c', p' c part_of c' and c' capable_of p and c capable_of p' and p' part_of p then c contributes_to p [RO]<br />
<br />
== Review Status ==<br />
Last reviewed: January 30, 2020<br />
<br />
[http://wiki.geneontology.org/index.php/Annotation_Relations Back to: Annotation Relations]<br />
<br />
[[Category: Gene Product to Term Relations]]</div>Hla28https://wiki.geneontology.org/index.php?title=Contributes_to&diff=79303Contributes to2020-12-15T13:28:33Z<p>Hla28: /* Definition */</p>
<hr />
<div><br />
== Definition ==<br />
A gene product is associated with a GO Molecular Function term using the qualifier 'contributes_to' when it is a member of a complex that is defined as an "irreducible molecular machine" - where a particular Molecular Function cannot be ascribed to an individual subunit or small set of subunits of a complex.<br />
<br />
== Range ==<br />
The 'contributes_to' qualifier can only be used with GO Molecular Function terms.<br />
<br />
== Child Terms ==<br />
None<br />
<br />
==Usage guidance==<br />
* The 'contributes_to' qualifier is used only in cases where a gene product does not perform a molecular function on its own, but as part of an "irreducible molecular machine" where the molecular function cannot be attributed to a subunit or group of subunits. Being part of a complex is not sufficient to use this qualifier. <br />
* In all cases, all intrinsic members of a complex should be annotated to 'part of' some 'GO:0032991 protein-containing complex' or an appropriate child term.<br />
* Checklist: useful questions: <br />
*# Can the activity occur without this subunit ? In this case maybe the annotation is not appropriate. <br />
*# Can the protein be annotated to another term ? Ideally each protein would have a MF. <br />
*# If the qualifier is omitted, is the annotation still acceptable ? (this is to avoid annotating for example regulatory subunits) <br />
<hr><br />
<br />
===Multiple subunits required for a molecular function===<br />
* All subunits of the complex should be assigned the activity using the 'contributes_to' qualifier if the complex can be described as an irreducible molecular machine. <br />
* For example, if a gene product is part of a complex but only has the function as part of that complex, e.g. forms a composite catalytic site that is required for the function, annotate to the molecular function using the qualifier 'contributes_to'. <br />
<br />
'''Examples'''<br />
<br />
1. '''ATP citrate lyase (ACL) in Chlorobaculum tepidum ''': a heterotetrameric enzyme composed of two distinct subunits, with residues from both subunits comprising the active site. Neither of the subunits expressed alone has ACL activity, but co-expression results in ACL activity. Both subunits contribute_to the ATP citrate lyase activity. '''Annotation for ATP citrate lyase subunit 1:'''<br />
Object: UniProt:Q8KDG1 (CT1089) <br />
Relation: contributes_to<br />
GO term: GO:0003878 ATP citrate synthase activity<br />
Evidence code: IDA<br />
PMID:16952946<br />
<br />
<br />
2. '''Subunits of nuclear RNA polymerases:''' none of the individual subunits have RNA polymerase activity, yet all of these subunits contribute_to DNA-dependent RNA polymerase activity. Note that there are gene products that are members of a nuclear RNA polymerase complex that serve other functions besides the polymerase activity. In these cases, the subunits would not be annotated to polymerase activity using the 'contributes to' qualifier. '''Annotation for ''S. pombe'' RNA polymerase II large subunit Rpb1:'''<br />
<br />
Object: SPBC28F2.12<br />
Relation: contributes_to<br />
GO term: GO:0001055 RNA polymerase II activity<br />
Evidence code: EXP<br />
PMID:9325316<br />
<br />
3. '''Subunits of ATP synthase complex ''': The molecular function as described by GO:0046933 'proton-transporting ATP synthase activity, rotational mechanism' cannot be performed by any individual subunit. The proton-transporting membrane sector (F0), the cytoplasmic sector (F1), that catalyzes ATP synthesis by a rotational mechanism, and the stator are required as part of an irreducible molecular machine to perform this function. In this case, all components the ATP synthase complex are annotated to GO:0046933 'proton-transporting ATP synthase activity, rotational mechanism' using the ‘contributes to’ qualifier. '''Annotation for ATP8 ATP synthase complex subunit:'''<br />
Object: SGD:S000007267 (ATP8)<br />
Relation: contributes_to<br />
GO term: GO:0046933 proton-transporting ATP synthase activity, rotational mechanism<br />
Evidence code: IDA<br />
PMID:20691145<br />
<br />
<hr><br />
<br />
===Multi-subunit complex in which the subunit necessary to perform the molecular function is not (yet) known===<br />
<br />
* If a gene product is part of a complex and it is unknown which subunit is responsible for the activity of the complex, do not annotate with a term from the Molecular Function branch of the GO, but use appropriate Cellular Component and Biological Process terms to capture biological knowledge accurately.<br />
<br />
<hr><br />
<br />
===When NOT to use 'contributes_to': single subunit required for a molecular function===<br />
* Being part of a complex does not mean that the molecular function necessarily requires multiple subunits: if a single subunit performs the molecular function, annotate the gene product to this function without any qualifier, but using relation 'enables (Protein2GO) or enabled by (Noctua)'.<br />
* If the gene product forms homomultimers, also annotate the gene product to this function without any qualifier.<br />
<br />
'''Examples'''<br />
Annotate the catalytic subunit, ''without'' the contributes_to qualifier. <br />
<br />
* '''eIF2''': has three subunits (alpha, beta, gamma); one binds GTP; one binds RNA; the whole complex binds the ribosome (all three subunits are required for ribosome binding). So one subunit is annotated to GTP binding and one to RNA binding without qualifiers, and all three stand in the contributes_to relationship to "ribosome binding". The molecular function annotations should have the extension 'occurs_in' eIF2 complex (GO:0005850), and all three are part_of the cellular component eIF2 complex (GO:0005850). <br />
** '''eIF2gamma''' is the actual GTPase, and eIF2alpha and -beta serving accessory functions. Therefore, eIF2gamma is annotated to GTPase activity; the alpha and beta subunits are '''not''' annotated to GTPase activity [https://www.ncbi.nlm.nih.gov/pubmed/29425030]<br />
<br />
* [http://amigo.geneontology.org/amigo/gene_product/UniProtKB:E2RG47 '''STT3'''] [https://www.ncbi.nlm.nih.gov/pubmed/PMID:12887896]: "dolichyl-diphosphooligosaccharide-protein glycotransferase activity": although it is a member of a complex, it is the catalytic subunit, so it should be annotated without the "contributes_to" qualifier.<br />
<br />
*'''PIGM-PIGX complex''': The PIGM-PIGX complex catalyzes GO:0000030 mannosyltransferase activity. PIGM is the sole catalytic subunit, and while the accessory PIGX subunit is required for activity, it does not have the activity [https://www.ncbi.nlm.nih.gov/pubmed/15635094]. <br />
** Therefore, only PIGM is annotated to GO:0000030 mannosyltransferase activity, without 'contributes_to'.<br />
<br />
* '''Prkag1 (protein kinase AMP-activated non-catalytic subunit gamma 1) [http://amigo.geneontology.org/amigo/gene_product/RGD:3388 RGD:3388]''': PMID:21399626 shows that the activation loop of the kinase domain is stabilized by the regulatory domain. The paper also shows that the regulatory subunit binds ADP, so it is really the subunit with a regulatory role. <br />
** annotation should be to "GO:0019887 protein kinase regulator activity"; Prkag1 does NOT contribute to "AMP-activated protein kinase activity".<br />
* '''Prkaa1 (protein kinase AMP-activated catalytic subunit alpha 1) [http://amigo.geneontology.org/amigo/gene_product/RGD:3388 RGD:3387]''' is the active subunit; is should be annotated to "AMP-activated protein kinase activity", without the "contributes_to" qualifier.<br />
<br />
==Specific cases==<br />
Other common functions for protein complex members: <br />
<br />
===Regulatory subunits===<br />
* If a gene product has been identified as the regulatory subunit of a complex, annotate to "X regulator activity" (GO:0098772 molecular function regulator or a child). Use 'has input' some 'gene product' to describe which gene product the annotated gene product regulates.<br />
*Need examples.<br />
<br />
===Adaptor subunits===<br />
* If a gene product is shown to bring together either a subunit of the complex with another protein, a substrate, a membrane, etc., this gene product may be anotated to GO:0060090 molecular adaptor activity or an appropriate child term.<br />
*Need examples.<br />
<br />
== Quality Control Checks ==<br />
<br />
== Relations Ontology ==<br />
[http://www.ontobee.org/ontology/RO?iri=http://purl.obolibrary.org/obo/RO_0002326 contributes to]<br />
<br />
*if and only if exists c', p' c part_of c' and c' capable_of p and c capable_of p' and p' part_of p then c contributes_to p [RO]<br />
<br />
== Review Status ==<br />
Last reviewed: January 30, 2020<br />
<br />
[http://wiki.geneontology.org/index.php/Annotation_Relations Back to: Annotation Relations]<br />
<br />
[[Category: Gene Product to Term Relations]]</div>Hla28https://wiki.geneontology.org/index.php?title=Contributes_to&diff=79302Contributes to2020-12-15T13:24:52Z<p>Hla28: /* Usage guidance */</p>
<hr />
<div><br />
== Definition ==<br />
A gene product is associated with a GO Molecular Function term using the qualifier 'contributes_to' when it is a member of a complex that is defined as an 'irreducible molecular machine' - where a particular Molecular Function cannot be ascribed to an individual subunit or small set of subunits of a complex.<br />
<br />
== Range ==<br />
The 'contributes_to' qualifier can only be used with GO Molecular Function terms.<br />
<br />
== Child Terms ==<br />
None<br />
<br />
==Usage guidance==<br />
* The 'contributes_to' qualifier is used only in cases where a gene product does not perform a molecular function on its own, but as part of an "irreducible molecular machine" where the molecular function cannot be attributed to a subunit or group of subunits. Being part of a complex is not sufficient to use this qualifier. <br />
* In all cases, all intrinsic members of a complex should be annotated to 'part of' some 'GO:0032991 protein-containing complex' or an appropriate child term.<br />
* Checklist: useful questions: <br />
*# Can the activity occur without this subunit ? In this case maybe the annotation is not appropriate. <br />
*# Can the protein be annotated to another term ? Ideally each protein would have a MF. <br />
*# If the qualifier is omitted, is the annotation still acceptable ? (this is to avoid annotating for example regulatory subunits) <br />
<hr><br />
<br />
===Multiple subunits required for a molecular function===<br />
* All subunits of the complex should be assigned the activity using the 'contributes_to' qualifier if the complex can be described as an irreducible molecular machine. <br />
* For example, if a gene product is part of a complex but only has the function as part of that complex, e.g. forms a composite catalytic site that is required for the function, annotate to the molecular function using the qualifier 'contributes_to'. <br />
<br />
'''Examples'''<br />
<br />
1. '''ATP citrate lyase (ACL) in Chlorobaculum tepidum ''': a heterotetrameric enzyme composed of two distinct subunits, with residues from both subunits comprising the active site. Neither of the subunits expressed alone has ACL activity, but co-expression results in ACL activity. Both subunits contribute_to the ATP citrate lyase activity. '''Annotation for ATP citrate lyase subunit 1:'''<br />
Object: UniProt:Q8KDG1 (CT1089) <br />
Relation: contributes_to<br />
GO term: GO:0003878 ATP citrate synthase activity<br />
Evidence code: IDA<br />
PMID:16952946<br />
<br />
<br />
2. '''Subunits of nuclear RNA polymerases:''' none of the individual subunits have RNA polymerase activity, yet all of these subunits contribute_to DNA-dependent RNA polymerase activity. Note that there are gene products that are members of a nuclear RNA polymerase complex that serve other functions besides the polymerase activity. In these cases, the subunits would not be annotated to polymerase activity using the 'contributes to' qualifier. '''Annotation for ''S. pombe'' RNA polymerase II large subunit Rpb1:'''<br />
<br />
Object: SPBC28F2.12<br />
Relation: contributes_to<br />
GO term: GO:0001055 RNA polymerase II activity<br />
Evidence code: EXP<br />
PMID:9325316<br />
<br />
3. '''Subunits of ATP synthase complex ''': The molecular function as described by GO:0046933 'proton-transporting ATP synthase activity, rotational mechanism' cannot be performed by any individual subunit. The proton-transporting membrane sector (F0), the cytoplasmic sector (F1), that catalyzes ATP synthesis by a rotational mechanism, and the stator are required as part of an irreducible molecular machine to perform this function. In this case, all components the ATP synthase complex are annotated to GO:0046933 'proton-transporting ATP synthase activity, rotational mechanism' using the ‘contributes to’ qualifier. '''Annotation for ATP8 ATP synthase complex subunit:'''<br />
Object: SGD:S000007267 (ATP8)<br />
Relation: contributes_to<br />
GO term: GO:0046933 proton-transporting ATP synthase activity, rotational mechanism<br />
Evidence code: IDA<br />
PMID:20691145<br />
<br />
<hr><br />
<br />
===Multi-subunit complex in which the subunit necessary to perform the molecular function is not (yet) known===<br />
<br />
* If a gene product is part of a complex and it is unknown which subunit is responsible for the activity of the complex, do not annotate with a term from the Molecular Function branch of the GO, but use appropriate Cellular Component and Biological Process terms to capture biological knowledge accurately.<br />
<br />
<hr><br />
<br />
===When NOT to use 'contributes_to': single subunit required for a molecular function===<br />
* Being part of a complex does not mean that the molecular function necessarily requires multiple subunits: if a single subunit performs the molecular function, annotate the gene product to this function without any qualifier, but using relation 'enables (Protein2GO) or enabled by (Noctua)'.<br />
* If the gene product forms homomultimers, also annotate the gene product to this function without any qualifier.<br />
<br />
'''Examples'''<br />
Annotate the catalytic subunit, ''without'' the contributes_to qualifier. <br />
<br />
* '''eIF2''': has three subunits (alpha, beta, gamma); one binds GTP; one binds RNA; the whole complex binds the ribosome (all three subunits are required for ribosome binding). So one subunit is annotated to GTP binding and one to RNA binding without qualifiers, and all three stand in the contributes_to relationship to "ribosome binding". The molecular function annotations should have the extension 'occurs_in' eIF2 complex (GO:0005850), and all three are part_of the cellular component eIF2 complex (GO:0005850). <br />
** '''eIF2gamma''' is the actual GTPase, and eIF2alpha and -beta serving accessory functions. Therefore, eIF2gamma is annotated to GTPase activity; the alpha and beta subunits are '''not''' annotated to GTPase activity [https://www.ncbi.nlm.nih.gov/pubmed/29425030]<br />
<br />
* [http://amigo.geneontology.org/amigo/gene_product/UniProtKB:E2RG47 '''STT3'''] [https://www.ncbi.nlm.nih.gov/pubmed/PMID:12887896]: "dolichyl-diphosphooligosaccharide-protein glycotransferase activity": although it is a member of a complex, it is the catalytic subunit, so it should be annotated without the "contributes_to" qualifier.<br />
<br />
*'''PIGM-PIGX complex''': The PIGM-PIGX complex catalyzes GO:0000030 mannosyltransferase activity. PIGM is the sole catalytic subunit, and while the accessory PIGX subunit is required for activity, it does not have the activity [https://www.ncbi.nlm.nih.gov/pubmed/15635094]. <br />
** Therefore, only PIGM is annotated to GO:0000030 mannosyltransferase activity, without 'contributes_to'.<br />
<br />
* '''Prkag1 (protein kinase AMP-activated non-catalytic subunit gamma 1) [http://amigo.geneontology.org/amigo/gene_product/RGD:3388 RGD:3388]''': PMID:21399626 shows that the activation loop of the kinase domain is stabilized by the regulatory domain. The paper also shows that the regulatory subunit binds ADP, so it is really the subunit with a regulatory role. <br />
** annotation should be to "GO:0019887 protein kinase regulator activity"; Prkag1 does NOT contribute to "AMP-activated protein kinase activity".<br />
* '''Prkaa1 (protein kinase AMP-activated catalytic subunit alpha 1) [http://amigo.geneontology.org/amigo/gene_product/RGD:3388 RGD:3387]''' is the active subunit; is should be annotated to "AMP-activated protein kinase activity", without the "contributes_to" qualifier.<br />
<br />
==Specific cases==<br />
Other common functions for protein complex members: <br />
<br />
===Regulatory subunits===<br />
* If a gene product has been identified as the regulatory subunit of a complex, annotate to "X regulator activity" (GO:0098772 molecular function regulator or a child). Use 'has input' some 'gene product' to describe which gene product the annotated gene product regulates.<br />
*Need examples.<br />
<br />
===Adaptor subunits===<br />
* If a gene product is shown to bring together either a subunit of the complex with another protein, a substrate, a membrane, etc., this gene product may be anotated to GO:0060090 molecular adaptor activity or an appropriate child term.<br />
*Need examples.<br />
<br />
== Quality Control Checks ==<br />
<br />
== Relations Ontology ==<br />
[http://www.ontobee.org/ontology/RO?iri=http://purl.obolibrary.org/obo/RO_0002326 contributes to]<br />
<br />
*if and only if exists c', p' c part_of c' and c' capable_of p and c capable_of p' and p' part_of p then c contributes_to p [RO]<br />
<br />
== Review Status ==<br />
Last reviewed: January 30, 2020<br />
<br />
[http://wiki.geneontology.org/index.php/Annotation_Relations Back to: Annotation Relations]<br />
<br />
[[Category: Gene Product to Term Relations]]</div>Hla28https://wiki.geneontology.org/index.php?title=Contributes_to&diff=79301Contributes to2020-12-15T13:24:29Z<p>Hla28: /* Definition */</p>
<hr />
<div><br />
== Definition ==<br />
A gene product is associated with a GO Molecular Function term using the qualifier 'contributes_to' when it is a member of a complex that is defined as an 'irreducible molecular machine' - where a particular Molecular Function cannot be ascribed to an individual subunit or small set of subunits of a complex.<br />
<br />
== Range ==<br />
The 'contributes_to' qualifier can only be used with GO Molecular Function terms.<br />
<br />
== Child Terms ==<br />
None<br />
<br />
==Usage guidance==<br />
* The 'contributes_to' qualifier is used only in cases where a gene product does not perform a molecular function on its own, but as part of an irreducible molecular machine where the molecular function cannot be attributed to a subunit or group of subunits. Being part of a complex is not sufficient to use this qualifier. <br />
* In all cases, all intrinsic members of a complex should be annotated to 'part of' some 'GO:0032991 protein-containing complex' or an appropriate child term.<br />
* Checklist: useful questions: <br />
*# Can the activity occur without this subunit ? In this case maybe the annotation is not appropriate. <br />
*# Can the protein be annotated to another term ? Ideally each protein would have a MF. <br />
*# If the qualifier is omitted, is the annotation still acceptable ? (this is to avoid annotating for example regulatory subunits) <br />
<hr><br />
<br />
===Multiple subunits required for a molecular function===<br />
* All subunits of the complex should be assigned the activity using the 'contributes_to' qualifier if the complex can be described as an irreducible molecular machine. <br />
* For example, if a gene product is part of a complex but only has the function as part of that complex, e.g. forms a composite catalytic site that is required for the function, annotate to the molecular function using the qualifier 'contributes_to'. <br />
<br />
'''Examples'''<br />
<br />
1. '''ATP citrate lyase (ACL) in Chlorobaculum tepidum ''': a heterotetrameric enzyme composed of two distinct subunits, with residues from both subunits comprising the active site. Neither of the subunits expressed alone has ACL activity, but co-expression results in ACL activity. Both subunits contribute_to the ATP citrate lyase activity. '''Annotation for ATP citrate lyase subunit 1:'''<br />
Object: UniProt:Q8KDG1 (CT1089) <br />
Relation: contributes_to<br />
GO term: GO:0003878 ATP citrate synthase activity<br />
Evidence code: IDA<br />
PMID:16952946<br />
<br />
<br />
2. '''Subunits of nuclear RNA polymerases:''' none of the individual subunits have RNA polymerase activity, yet all of these subunits contribute_to DNA-dependent RNA polymerase activity. Note that there are gene products that are members of a nuclear RNA polymerase complex that serve other functions besides the polymerase activity. In these cases, the subunits would not be annotated to polymerase activity using the 'contributes to' qualifier. '''Annotation for ''S. pombe'' RNA polymerase II large subunit Rpb1:'''<br />
<br />
Object: SPBC28F2.12<br />
Relation: contributes_to<br />
GO term: GO:0001055 RNA polymerase II activity<br />
Evidence code: EXP<br />
PMID:9325316<br />
<br />
3. '''Subunits of ATP synthase complex ''': The molecular function as described by GO:0046933 'proton-transporting ATP synthase activity, rotational mechanism' cannot be performed by any individual subunit. The proton-transporting membrane sector (F0), the cytoplasmic sector (F1), that catalyzes ATP synthesis by a rotational mechanism, and the stator are required as part of an irreducible molecular machine to perform this function. In this case, all components the ATP synthase complex are annotated to GO:0046933 'proton-transporting ATP synthase activity, rotational mechanism' using the ‘contributes to’ qualifier. '''Annotation for ATP8 ATP synthase complex subunit:'''<br />
Object: SGD:S000007267 (ATP8)<br />
Relation: contributes_to<br />
GO term: GO:0046933 proton-transporting ATP synthase activity, rotational mechanism<br />
Evidence code: IDA<br />
PMID:20691145<br />
<br />
<hr><br />
<br />
===Multi-subunit complex in which the subunit necessary to perform the molecular function is not (yet) known===<br />
<br />
* If a gene product is part of a complex and it is unknown which subunit is responsible for the activity of the complex, do not annotate with a term from the Molecular Function branch of the GO, but use appropriate Cellular Component and Biological Process terms to capture biological knowledge accurately.<br />
<br />
<hr><br />
<br />
===When NOT to use 'contributes_to': single subunit required for a molecular function===<br />
* Being part of a complex does not mean that the molecular function necessarily requires multiple subunits: if a single subunit performs the molecular function, annotate the gene product to this function without any qualifier, but using relation 'enables (Protein2GO) or enabled by (Noctua)'.<br />
* If the gene product forms homomultimers, also annotate the gene product to this function without any qualifier.<br />
<br />
'''Examples'''<br />
Annotate the catalytic subunit, ''without'' the contributes_to qualifier. <br />
<br />
* '''eIF2''': has three subunits (alpha, beta, gamma); one binds GTP; one binds RNA; the whole complex binds the ribosome (all three subunits are required for ribosome binding). So one subunit is annotated to GTP binding and one to RNA binding without qualifiers, and all three stand in the contributes_to relationship to "ribosome binding". The molecular function annotations should have the extension 'occurs_in' eIF2 complex (GO:0005850), and all three are part_of the cellular component eIF2 complex (GO:0005850). <br />
** '''eIF2gamma''' is the actual GTPase, and eIF2alpha and -beta serving accessory functions. Therefore, eIF2gamma is annotated to GTPase activity; the alpha and beta subunits are '''not''' annotated to GTPase activity [https://www.ncbi.nlm.nih.gov/pubmed/29425030]<br />
<br />
* [http://amigo.geneontology.org/amigo/gene_product/UniProtKB:E2RG47 '''STT3'''] [https://www.ncbi.nlm.nih.gov/pubmed/PMID:12887896]: "dolichyl-diphosphooligosaccharide-protein glycotransferase activity": although it is a member of a complex, it is the catalytic subunit, so it should be annotated without the "contributes_to" qualifier.<br />
<br />
*'''PIGM-PIGX complex''': The PIGM-PIGX complex catalyzes GO:0000030 mannosyltransferase activity. PIGM is the sole catalytic subunit, and while the accessory PIGX subunit is required for activity, it does not have the activity [https://www.ncbi.nlm.nih.gov/pubmed/15635094]. <br />
** Therefore, only PIGM is annotated to GO:0000030 mannosyltransferase activity, without 'contributes_to'.<br />
<br />
* '''Prkag1 (protein kinase AMP-activated non-catalytic subunit gamma 1) [http://amigo.geneontology.org/amigo/gene_product/RGD:3388 RGD:3388]''': PMID:21399626 shows that the activation loop of the kinase domain is stabilized by the regulatory domain. The paper also shows that the regulatory subunit binds ADP, so it is really the subunit with a regulatory role. <br />
** annotation should be to "GO:0019887 protein kinase regulator activity"; Prkag1 does NOT contribute to "AMP-activated protein kinase activity".<br />
* '''Prkaa1 (protein kinase AMP-activated catalytic subunit alpha 1) [http://amigo.geneontology.org/amigo/gene_product/RGD:3388 RGD:3387]''' is the active subunit; is should be annotated to "AMP-activated protein kinase activity", without the "contributes_to" qualifier.<br />
<br />
==Specific cases==<br />
Other common functions for protein complex members: <br />
<br />
===Regulatory subunits===<br />
* If a gene product has been identified as the regulatory subunit of a complex, annotate to "X regulator activity" (GO:0098772 molecular function regulator or a child). Use 'has input' some 'gene product' to describe which gene product the annotated gene product regulates.<br />
*Need examples.<br />
<br />
===Adaptor subunits===<br />
* If a gene product is shown to bring together either a subunit of the complex with another protein, a substrate, a membrane, etc., this gene product may be anotated to GO:0060090 molecular adaptor activity or an appropriate child term.<br />
*Need examples.<br />
<br />
== Quality Control Checks ==<br />
<br />
== Relations Ontology ==<br />
[http://www.ontobee.org/ontology/RO?iri=http://purl.obolibrary.org/obo/RO_0002326 contributes to]<br />
<br />
*if and only if exists c', p' c part_of c' and c' capable_of p and c capable_of p' and p' part_of p then c contributes_to p [RO]<br />
<br />
== Review Status ==<br />
Last reviewed: January 30, 2020<br />
<br />
[http://wiki.geneontology.org/index.php/Annotation_Relations Back to: Annotation Relations]<br />
<br />
[[Category: Gene Product to Term Relations]]</div>Hla28https://wiki.geneontology.org/index.php?title=Contributes_to&diff=78285Contributes to2020-06-09T11:10:11Z<p>Hla28: /* Multi-subunit complex in which the subunit necessary to perform the molecular function is not (yet) known */</p>
<hr />
<div><br />
== Definition ==<br />
A gene product is associated with a GO Molecular Function term using the qualifier 'contributes_to' when it is a member of a complex that is defined as an irreducible molecular machine' - where a particular Molecular Function cannot be ascribed to an individual subunit(s) of a complex.<br />
<br />
== Range ==<br />
The 'contributes_to' qualifier can only be used with GO Molecular Function terms.<br />
<br />
== Child Terms ==<br />
None<br />
<br />
==Usage guidance==<br />
* The 'contributes_to' qualifier is used only in cases where a gene product does not perform a molecular function on its own, but as part of an irreducible molecular machine where the molecular function cannot be attributed to a subunit or group of subunits. Being part of a complex is not sufficient to use this qualifier. <br />
* In all cases, all intrinsic members of a complex should be annotated to 'part of' some 'GO:0032991 protein-containing complex' or an appropriate child term.<br />
<br />
<hr><br />
<br />
===Multiple subunits required for a molecular function===<br />
* All subunits of the complex should be assigned the activity using the 'contributes_to' qualifier if the complex can be described as an irreducible molecular machine. <br />
* For example, if a gene product is part of a complex but only has the function as part of that complex, e.g. forms a composite catalytic site that is required for the function, annotate to the molecular function using the qualifier 'contributes_to'. <br />
<br />
'''Examples'''<br />
<br />
1. '''ATP citrate lyase (ACL) in Chlorobaculum tepidum ''': a heterotetrameric enzyme composed of two distinct subunits, with residues from both subunits comprising the active site. Neither of the subunits expressed alone has ACL activity, but co-expression results in ACL activity. Both subunits contribute_to the ATP citrate lyase activity. '''Annotation for ATP citrate lyase subunit 1:'''<br />
Object: UniProt:Q8KDG1 (CT1089) <br />
Relation: contributes_to<br />
GO term: GO:0003878 ATP citrate synthase activity<br />
Evidence code: IDA<br />
PMID:16952946<br />
<br />
<br />
2. '''Subunits of nuclear RNA polymerases:''' none of the individual subunits have RNA polymerase activity, yet all of these subunits contribute_to DNA-dependent RNA polymerase activity. Note that there are gene products that are members of a nuclear RNA polymerase complex that serve other functions besides the polymerase activity. In these cases, the subunits would not be annotated to polymerase activity using the 'contributes to' qualifier. '''Annotation for ''S. pombe'' RNA polymerase II large subunit Rpb1:'''<br />
<br />
Object: SPBC28F2.12<br />
Relation: contributes_to<br />
GO term: GO:0001055 RNA polymerase II activity<br />
Evidence code: EXP<br />
PMID:9325316<br />
<br />
3. '''Subunits of ATP synthase complex ''': The molecular function as described by GO:0046933 'proton-transporting ATP synthase activity, rotational mechanism' cannot be performed by any individual subunit. The proton-transporting membrane sector (F0), the cytoplasmic sector (F1), that catalyzes ATP synthesis by a rotational mechanism, and the stator are required as part of an irreducible molecular machine to perform this function. In this case, all components the ATP synthase complex are annotated to GO:0046933 'proton-transporting ATP synthase activity, rotational mechanism' using the ‘contributes to’ qualifier. '''Annotation for ATP8 ATP synthase complex subunit:'''<br />
Object: SGD:S000007267 (ATP8)<br />
Relation: contributes_to<br />
GO term: GO:0046933 proton-transporting ATP synthase activity, rotational mechanism<br />
Evidence code: IDA<br />
PMID:20691145<br />
<br />
<hr><br />
<br />
===Multi-subunit complex in which the subunit necessary to perform the molecular function is not (yet) known===<br />
<br />
* If a gene product is part of a complex and it is unknown which subunit is responsible for the activity of the complex, do not annotate with a term from the Molecular Function branch of the GO, but use appropriate Cellular Component and Biological Process terms to capture biological knowledge accurately.<br />
<br />
<hr><br />
<br />
===When NOT to use 'contributes_to': single subunit required for a molecular function===<br />
* Being part of a complex does not mean that the molecular function necessarily requires multiple subunits: if a single subunit performs the molecular function, annotate the gene product to this function without any qualifier, but using relation 'enables (Protein2GO) or enabled by (Noctua)'.<br />
* If the gene product forms homomultimers, also annotate the gene product to this function without any qualifier.<br />
<br />
'''Examples'''<br />
Annotate the catalytic subunit, ''without'' the contributes_to qualifier. <br />
<br />
* '''eIF2''': has three subunits (alpha, beta, gamma); one binds GTP; one binds RNA; the whole complex binds the ribosome (all three subunits are required for ribosome binding). So one subunit is annotated to GTP binding and one to RNA binding without qualifiers, and all three stand in the contributes_to relationship to "ribosome binding". The molecular function annotations should have the extension 'occurs_in' eIF2 complex (GO:0005850), and all three are part_of the cellular component eIF2 complex (GO:0005850). <br />
** '''eIF2gamma''' is the actual GTPase, and eIF2alpha and -beta serving accessory functions. Therefore, eIF2gamma is annotated to GTPase activity; the alpha and beta subunits are '''not''' annotated to GTPase activity [https://www.ncbi.nlm.nih.gov/pubmed/29425030]<br />
<br />
* [http://amigo.geneontology.org/amigo/gene_product/UniProtKB:E2RG47 '''STT3'''] [https://www.ncbi.nlm.nih.gov/pubmed/PMID:12887896]: "dolichyl-diphosphooligosaccharide-protein glycotransferase activity": although it is a member of a complex, it is the catalytic subunit, so it should be annotated without the "contributes_to" qualifier.<br />
<br />
*'''PIGM-PIGX complex''': The PIGM-PIGX complex catalyzes GO:0000030 mannosyltransferase activity. PIGM is the sole catalytic subunit, and while the accessory PIGX subunit is required for activity, it does not have the activity [https://www.ncbi.nlm.nih.gov/pubmed/15635094]. <br />
** Therefore, only PIGM is annotated to GO:0000030 mannosyltransferase activity, without 'contributes_to'.<br />
<br />
* '''Prkag1 (protein kinase AMP-activated non-catalytic subunit gamma 1) [http://amigo.geneontology.org/amigo/gene_product/RGD:3388 RGD:3388]''': PMID:21399626 shows that the activation loop of the kinase domain is stabilized by the regulatory domain. The paper also shows that the regulatory subunit binds ADP, so it is really the subunit with a regulatory role. <br />
** annotation should be to "GO:0019887 protein kinase regulator activity"; Prkag1 does NOT contribute to "AMP-activated protein kinase activity".<br />
* '''Prkaa1 (protein kinase AMP-activated catalytic subunit alpha 1) [http://amigo.geneontology.org/amigo/gene_product/RGD:3388 RGD:3387]''' is the active subunit; is should be annotated to "AMP-activated protein kinase activity", without the "contributes_to" qualifier.<br />
<br />
==Specific cases==<br />
Other common functions for protein complex members: <br />
<br />
===Regulatory subunits===<br />
* If a gene product has been identified as the regulatory subunit of a complex, annotate to "X regulator activity" (GO:0098772 molecular function regulator or a child). Use 'has input' some 'gene product' to describe which gene product the annotated gene product regulates.<br />
*Need examples.<br />
<br />
===Adaptor subunits===<br />
* If a gene product is shown to bring together either a subunit of the complex with another protein, a substrate, a membrane, etc., this gene product may be anotated to GO:0060090 molecular adaptor activity or an appropriate child term.<br />
*Need examples.<br />
<br />
== Quality Control Checks ==<br />
<br />
== Relations Ontology ==<br />
[http://www.ontobee.org/ontology/RO?iri=http://purl.obolibrary.org/obo/RO_0002326 contributes to]<br />
<br />
*if and only if exists c', p' c part_of c' and c' capable_of p and c capable_of p' and p' part_of p then c contributes_to p [RO]<br />
<br />
== Review Status ==<br />
Last reviewed: January 30, 2020<br />
<br />
[http://wiki.geneontology.org/index.php/Annotation_Relations Back to: Annotation Relations]<br />
<br />
[[Category: Gene Product to Term Relations]]</div>Hla28https://wiki.geneontology.org/index.php?title=Contributes_to&diff=78284Contributes to2020-06-09T11:09:38Z<p>Hla28: /* Multi-subunit complex in which the subunit necessary to perform the molecular function is not (yet) known */</p>
<hr />
<div><br />
== Definition ==<br />
A gene product is associated with a GO Molecular Function term using the qualifier 'contributes_to' when it is a member of a complex that is defined as an irreducible molecular machine' - where a particular Molecular Function cannot be ascribed to an individual subunit(s) of a complex.<br />
<br />
== Range ==<br />
The 'contributes_to' qualifier can only be used with GO Molecular Function terms.<br />
<br />
== Child Terms ==<br />
None<br />
<br />
==Usage guidance==<br />
* The 'contributes_to' qualifier is used only in cases where a gene product does not perform a molecular function on its own, but as part of an irreducible molecular machine where the molecular function cannot be attributed to a subunit or group of subunits. Being part of a complex is not sufficient to use this qualifier. <br />
* In all cases, all intrinsic members of a complex should be annotated to 'part of' some 'GO:0032991 protein-containing complex' or an appropriate child term.<br />
<br />
<hr><br />
<br />
===Multiple subunits required for a molecular function===<br />
* All subunits of the complex should be assigned the activity using the 'contributes_to' qualifier if the complex can be described as an irreducible molecular machine. <br />
* For example, if a gene product is part of a complex but only has the function as part of that complex, e.g. forms a composite catalytic site that is required for the function, annotate to the molecular function using the qualifier 'contributes_to'. <br />
<br />
'''Examples'''<br />
<br />
1. '''ATP citrate lyase (ACL) in Chlorobaculum tepidum ''': a heterotetrameric enzyme composed of two distinct subunits, with residues from both subunits comprising the active site. Neither of the subunits expressed alone has ACL activity, but co-expression results in ACL activity. Both subunits contribute_to the ATP citrate lyase activity. '''Annotation for ATP citrate lyase subunit 1:'''<br />
Object: UniProt:Q8KDG1 (CT1089) <br />
Relation: contributes_to<br />
GO term: GO:0003878 ATP citrate synthase activity<br />
Evidence code: IDA<br />
PMID:16952946<br />
<br />
<br />
2. '''Subunits of nuclear RNA polymerases:''' none of the individual subunits have RNA polymerase activity, yet all of these subunits contribute_to DNA-dependent RNA polymerase activity. Note that there are gene products that are members of a nuclear RNA polymerase complex that serve other functions besides the polymerase activity. In these cases, the subunits would not be annotated to polymerase activity using the 'contributes to' qualifier. '''Annotation for ''S. pombe'' RNA polymerase II large subunit Rpb1:'''<br />
<br />
Object: SPBC28F2.12<br />
Relation: contributes_to<br />
GO term: GO:0001055 RNA polymerase II activity<br />
Evidence code: EXP<br />
PMID:9325316<br />
<br />
3. '''Subunits of ATP synthase complex ''': The molecular function as described by GO:0046933 'proton-transporting ATP synthase activity, rotational mechanism' cannot be performed by any individual subunit. The proton-transporting membrane sector (F0), the cytoplasmic sector (F1), that catalyzes ATP synthesis by a rotational mechanism, and the stator are required as part of an irreducible molecular machine to perform this function. In this case, all components the ATP synthase complex are annotated to GO:0046933 'proton-transporting ATP synthase activity, rotational mechanism' using the ‘contributes to’ qualifier. '''Annotation for ATP8 ATP synthase complex subunit:'''<br />
Object: SGD:S000007267 (ATP8)<br />
Relation: contributes_to<br />
GO term: GO:0046933 proton-transporting ATP synthase activity, rotational mechanism<br />
Evidence code: IDA<br />
PMID:20691145<br />
<br />
<hr><br />
<br />
===Multi-subunit complex in which the subunit necessary to perform the molecular function is not (yet) known===<br />
<br />
* If a gene product is part of a complex and it is unknown which subunit is responsible for the activity of the complex, do not annotate with a term from the Molecular Function branch of the GO, but use appropriate Cellular Component and Biological Process terms to capture the biological knowledge.<br />
<br />
<hr><br />
<br />
===When NOT to use 'contributes_to': single subunit required for a molecular function===<br />
* Being part of a complex does not mean that the molecular function necessarily requires multiple subunits: if a single subunit performs the molecular function, annotate the gene product to this function without any qualifier, but using relation 'enables (Protein2GO) or enabled by (Noctua)'.<br />
* If the gene product forms homomultimers, also annotate the gene product to this function without any qualifier.<br />
<br />
'''Examples'''<br />
Annotate the catalytic subunit, ''without'' the contributes_to qualifier. <br />
<br />
* '''eIF2''': has three subunits (alpha, beta, gamma); one binds GTP; one binds RNA; the whole complex binds the ribosome (all three subunits are required for ribosome binding). So one subunit is annotated to GTP binding and one to RNA binding without qualifiers, and all three stand in the contributes_to relationship to "ribosome binding". The molecular function annotations should have the extension 'occurs_in' eIF2 complex (GO:0005850), and all three are part_of the cellular component eIF2 complex (GO:0005850). <br />
** '''eIF2gamma''' is the actual GTPase, and eIF2alpha and -beta serving accessory functions. Therefore, eIF2gamma is annotated to GTPase activity; the alpha and beta subunits are '''not''' annotated to GTPase activity [https://www.ncbi.nlm.nih.gov/pubmed/29425030]<br />
<br />
* [http://amigo.geneontology.org/amigo/gene_product/UniProtKB:E2RG47 '''STT3'''] [https://www.ncbi.nlm.nih.gov/pubmed/PMID:12887896]: "dolichyl-diphosphooligosaccharide-protein glycotransferase activity": although it is a member of a complex, it is the catalytic subunit, so it should be annotated without the "contributes_to" qualifier.<br />
<br />
*'''PIGM-PIGX complex''': The PIGM-PIGX complex catalyzes GO:0000030 mannosyltransferase activity. PIGM is the sole catalytic subunit, and while the accessory PIGX subunit is required for activity, it does not have the activity [https://www.ncbi.nlm.nih.gov/pubmed/15635094]. <br />
** Therefore, only PIGM is annotated to GO:0000030 mannosyltransferase activity, without 'contributes_to'.<br />
<br />
* '''Prkag1 (protein kinase AMP-activated non-catalytic subunit gamma 1) [http://amigo.geneontology.org/amigo/gene_product/RGD:3388 RGD:3388]''': PMID:21399626 shows that the activation loop of the kinase domain is stabilized by the regulatory domain. The paper also shows that the regulatory subunit binds ADP, so it is really the subunit with a regulatory role. <br />
** annotation should be to "GO:0019887 protein kinase regulator activity"; Prkag1 does NOT contribute to "AMP-activated protein kinase activity".<br />
* '''Prkaa1 (protein kinase AMP-activated catalytic subunit alpha 1) [http://amigo.geneontology.org/amigo/gene_product/RGD:3388 RGD:3387]''' is the active subunit; is should be annotated to "AMP-activated protein kinase activity", without the "contributes_to" qualifier.<br />
<br />
==Specific cases==<br />
Other common functions for protein complex members: <br />
<br />
===Regulatory subunits===<br />
* If a gene product has been identified as the regulatory subunit of a complex, annotate to "X regulator activity" (GO:0098772 molecular function regulator or a child). Use 'has input' some 'gene product' to describe which gene product the annotated gene product regulates.<br />
*Need examples.<br />
<br />
===Adaptor subunits===<br />
* If a gene product is shown to bring together either a subunit of the complex with another protein, a substrate, a membrane, etc., this gene product may be anotated to GO:0060090 molecular adaptor activity or an appropriate child term.<br />
*Need examples.<br />
<br />
== Quality Control Checks ==<br />
<br />
== Relations Ontology ==<br />
[http://www.ontobee.org/ontology/RO?iri=http://purl.obolibrary.org/obo/RO_0002326 contributes to]<br />
<br />
*if and only if exists c', p' c part_of c' and c' capable_of p and c capable_of p' and p' part_of p then c contributes_to p [RO]<br />
<br />
== Review Status ==<br />
Last reviewed: January 30, 2020<br />
<br />
[http://wiki.geneontology.org/index.php/Annotation_Relations Back to: Annotation Relations]<br />
<br />
[[Category: Gene Product to Term Relations]]</div>Hla28https://wiki.geneontology.org/index.php?title=Contributes_to&diff=78283Contributes to2020-06-09T11:07:50Z<p>Hla28: /* Multiple subunits required for a molecular function */</p>
<hr />
<div><br />
== Definition ==<br />
A gene product is associated with a GO Molecular Function term using the qualifier 'contributes_to' when it is a member of a complex that is defined as an irreducible molecular machine' - where a particular Molecular Function cannot be ascribed to an individual subunit(s) of a complex.<br />
<br />
== Range ==<br />
The 'contributes_to' qualifier can only be used with GO Molecular Function terms.<br />
<br />
== Child Terms ==<br />
None<br />
<br />
==Usage guidance==<br />
* The 'contributes_to' qualifier is used only in cases where a gene product does not perform a molecular function on its own, but as part of an irreducible molecular machine where the molecular function cannot be attributed to a subunit or group of subunits. Being part of a complex is not sufficient to use this qualifier. <br />
* In all cases, all intrinsic members of a complex should be annotated to 'part of' some 'GO:0032991 protein-containing complex' or an appropriate child term.<br />
<br />
<hr><br />
<br />
===Multiple subunits required for a molecular function===<br />
* All subunits of the complex should be assigned the activity using the 'contributes_to' qualifier if the complex can be described as an irreducible molecular machine. <br />
* For example, if a gene product is part of a complex but only has the function as part of that complex, e.g. forms a composite catalytic site that is required for the function, annotate to the molecular function using the qualifier 'contributes_to'. <br />
<br />
'''Examples'''<br />
<br />
1. '''ATP citrate lyase (ACL) in Chlorobaculum tepidum ''': a heterotetrameric enzyme composed of two distinct subunits, with residues from both subunits comprising the active site. Neither of the subunits expressed alone has ACL activity, but co-expression results in ACL activity. Both subunits contribute_to the ATP citrate lyase activity. '''Annotation for ATP citrate lyase subunit 1:'''<br />
Object: UniProt:Q8KDG1 (CT1089) <br />
Relation: contributes_to<br />
GO term: GO:0003878 ATP citrate synthase activity<br />
Evidence code: IDA<br />
PMID:16952946<br />
<br />
<br />
2. '''Subunits of nuclear RNA polymerases:''' none of the individual subunits have RNA polymerase activity, yet all of these subunits contribute_to DNA-dependent RNA polymerase activity. Note that there are gene products that are members of a nuclear RNA polymerase complex that serve other functions besides the polymerase activity. In these cases, the subunits would not be annotated to polymerase activity using the 'contributes to' qualifier. '''Annotation for ''S. pombe'' RNA polymerase II large subunit Rpb1:'''<br />
<br />
Object: SPBC28F2.12<br />
Relation: contributes_to<br />
GO term: GO:0001055 RNA polymerase II activity<br />
Evidence code: EXP<br />
PMID:9325316<br />
<br />
3. '''Subunits of ATP synthase complex ''': The molecular function as described by GO:0046933 'proton-transporting ATP synthase activity, rotational mechanism' cannot be performed by any individual subunit. The proton-transporting membrane sector (F0), the cytoplasmic sector (F1), that catalyzes ATP synthesis by a rotational mechanism, and the stator are required as part of an irreducible molecular machine to perform this function. In this case, all components the ATP synthase complex are annotated to GO:0046933 'proton-transporting ATP synthase activity, rotational mechanism' using the ‘contributes to’ qualifier. '''Annotation for ATP8 ATP synthase complex subunit:'''<br />
Object: SGD:S000007267 (ATP8)<br />
Relation: contributes_to<br />
GO term: GO:0046933 proton-transporting ATP synthase activity, rotational mechanism<br />
Evidence code: IDA<br />
PMID:20691145<br />
<br />
<hr><br />
<br />
===Multi-subunit complex in which the subunit necessary to perform the molecular function is not (yet) known===<br />
<br />
* If a gene product is part of a complex and it is unknown which subunit is responsible for the activity of the complex, annotate all gene products to the molecular function using the qualifier 'contributes_to'. <br />
*Need examples.<br />
<br />
<hr><br />
<br />
===When NOT to use 'contributes_to': single subunit required for a molecular function===<br />
* Being part of a complex does not mean that the molecular function necessarily requires multiple subunits: if a single subunit performs the molecular function, annotate the gene product to this function without any qualifier, but using relation 'enables (Protein2GO) or enabled by (Noctua)'.<br />
* If the gene product forms homomultimers, also annotate the gene product to this function without any qualifier.<br />
<br />
'''Examples'''<br />
Annotate the catalytic subunit, ''without'' the contributes_to qualifier. <br />
<br />
* '''eIF2''': has three subunits (alpha, beta, gamma); one binds GTP; one binds RNA; the whole complex binds the ribosome (all three subunits are required for ribosome binding). So one subunit is annotated to GTP binding and one to RNA binding without qualifiers, and all three stand in the contributes_to relationship to "ribosome binding". The molecular function annotations should have the extension 'occurs_in' eIF2 complex (GO:0005850), and all three are part_of the cellular component eIF2 complex (GO:0005850). <br />
** '''eIF2gamma''' is the actual GTPase, and eIF2alpha and -beta serving accessory functions. Therefore, eIF2gamma is annotated to GTPase activity; the alpha and beta subunits are '''not''' annotated to GTPase activity [https://www.ncbi.nlm.nih.gov/pubmed/29425030]<br />
<br />
* [http://amigo.geneontology.org/amigo/gene_product/UniProtKB:E2RG47 '''STT3'''] [https://www.ncbi.nlm.nih.gov/pubmed/PMID:12887896]: "dolichyl-diphosphooligosaccharide-protein glycotransferase activity": although it is a member of a complex, it is the catalytic subunit, so it should be annotated without the "contributes_to" qualifier.<br />
<br />
*'''PIGM-PIGX complex''': The PIGM-PIGX complex catalyzes GO:0000030 mannosyltransferase activity. PIGM is the sole catalytic subunit, and while the accessory PIGX subunit is required for activity, it does not have the activity [https://www.ncbi.nlm.nih.gov/pubmed/15635094]. <br />
** Therefore, only PIGM is annotated to GO:0000030 mannosyltransferase activity, without 'contributes_to'.<br />
<br />
* '''Prkag1 (protein kinase AMP-activated non-catalytic subunit gamma 1) [http://amigo.geneontology.org/amigo/gene_product/RGD:3388 RGD:3388]''': PMID:21399626 shows that the activation loop of the kinase domain is stabilized by the regulatory domain. The paper also shows that the regulatory subunit binds ADP, so it is really the subunit with a regulatory role. <br />
** annotation should be to "GO:0019887 protein kinase regulator activity"; Prkag1 does NOT contribute to "AMP-activated protein kinase activity".<br />
* '''Prkaa1 (protein kinase AMP-activated catalytic subunit alpha 1) [http://amigo.geneontology.org/amigo/gene_product/RGD:3388 RGD:3387]''' is the active subunit; is should be annotated to "AMP-activated protein kinase activity", without the "contributes_to" qualifier.<br />
<br />
==Specific cases==<br />
Other common functions for protein complex members: <br />
<br />
===Regulatory subunits===<br />
* If a gene product has been identified as the regulatory subunit of a complex, annotate to "X regulator activity" (GO:0098772 molecular function regulator or a child). Use 'has input' some 'gene product' to describe which gene product the annotated gene product regulates.<br />
*Need examples.<br />
<br />
===Adaptor subunits===<br />
* If a gene product is shown to bring together either a subunit of the complex with another protein, a substrate, a membrane, etc., this gene product may be anotated to GO:0060090 molecular adaptor activity or an appropriate child term.<br />
*Need examples.<br />
<br />
== Quality Control Checks ==<br />
<br />
== Relations Ontology ==<br />
[http://www.ontobee.org/ontology/RO?iri=http://purl.obolibrary.org/obo/RO_0002326 contributes to]<br />
<br />
*if and only if exists c', p' c part_of c' and c' capable_of p and c capable_of p' and p' part_of p then c contributes_to p [RO]<br />
<br />
== Review Status ==<br />
Last reviewed: January 30, 2020<br />
<br />
[http://wiki.geneontology.org/index.php/Annotation_Relations Back to: Annotation Relations]<br />
<br />
[[Category: Gene Product to Term Relations]]</div>Hla28https://wiki.geneontology.org/index.php?title=Contributes_to&diff=78282Contributes to2020-06-09T10:52:45Z<p>Hla28: /* Multiple subunits required for a molecular function */</p>
<hr />
<div><br />
== Definition ==<br />
A gene product is associated with a GO Molecular Function term using the qualifier 'contributes_to' when it is a member of a complex that is defined as an irreducible molecular machine' - where a particular Molecular Function cannot be ascribed to an individual subunit(s) of a complex.<br />
<br />
== Range ==<br />
The 'contributes_to' qualifier can only be used with GO Molecular Function terms.<br />
<br />
== Child Terms ==<br />
None<br />
<br />
==Usage guidance==<br />
* The 'contributes_to' qualifier is used only in cases where a gene product does not perform a molecular function on its own, but as part of an irreducible molecular machine where the molecular function cannot be attributed to a subunit or group of subunits. Being part of a complex is not sufficient to use this qualifier. <br />
* In all cases, all intrinsic members of a complex should be annotated to 'part of' some 'GO:0032991 protein-containing complex' or an appropriate child term.<br />
<br />
<hr><br />
<br />
===Multiple subunits required for a molecular function===<br />
* All subunits of the complex should be assigned the activity using the 'contributes_to' qualifier if the complex can be described as an irreducible molecular machine. <br />
* For example, if a gene product is part of a complex but only has the function as part of that complex, e.g. forms a composite catalytic site that is required for the function, annotate to the molecular function using the qualifier 'contributes_to'. <br />
<br />
'''Examples'''<br />
<br />
1. '''ATP citrate lyase (ACL) in Chlorobaculum tepidum ''': a heterotetrameric enzyme composed of two distinct subunits, with residues from both subunits comprising the active site. Neither of the subunits expressed alone has ACL activity, but co-expression results in ACL activity. Both subunits contribute_to the ATP citrate lyase activity. '''Annotation for ATP citrate lyase subunit 1:'''<br />
Object: UniProt:Q8KDG1 (CT1089) <br />
Relation: contributes_to<br />
GO term: GO:0003878 ATP citrate synthase activity<br />
Evidence code: IDA<br />
PMID:16952946<br />
<br />
<br />
2. '''Subunits of nuclear RNA polymerases:''' none of the individual subunits have RNA polymerase activity, yet all of these subunits contribute_to DNA-dependent RNA polymerase activity. Note that there are gene products that are members of a nuclear RNA polymerase complex that serve other functions besides the polymerase activity. In these cases, the subunits would not be annotated to polymerase activity using the 'contributes to' qualifier. '''Annotation for ''S. pombe'' RNA polymerase II large subunit Rpb1:'''<br />
<br />
Object: SPBC28F2.12<br />
Relation: contributes_to<br />
GO term: GO:0001055 RNA polymerase II activity<br />
Evidence code: EXP<br />
PMID:9325316<br />
<br />
3. '''MBF transcription factor complex''': res2 and cdc10 are both members of the Schizosaccharomyces pombe MBF transcription factor complex. Each contains, by sequence analysis, a predicted DNA-binding domain. In vitro assays, however, show that neither subunit binds DNA alone; DNA-binding activity is only detectable when the subunits are co-expressed. In this case, res2 and cdc10 are both annotated to GO:0000978 ‘RNA polymerase II cis-regulatory region sequence-specific DNA binding ’ using the ‘contributes to’ qualifier. '''Annotation for res2 MBF complex subunit:'''<br />
Object: PomBase:SPAC22F3.09c (res2)<br />
Relation: contributes_to<br />
GO term: GO:0000978 RNA polymerase II cis-regulatory region sequence-specific DNA binding <br />
Evidence code: IDA<br />
PMID:7926774<br />
<br />
<hr><br />
<br />
===Multi-subunit complex in which the subunit necessary to perform the molecular function is not (yet) known===<br />
<br />
* If a gene product is part of a complex and it is unknown which subunit is responsible for the activity of the complex, annotate all gene products to the molecular function using the qualifier 'contributes_to'. <br />
*Need examples.<br />
<br />
<hr><br />
<br />
===When NOT to use 'contributes_to': single subunit required for a molecular function===<br />
* Being part of a complex does not mean that the molecular function necessarily requires multiple subunits: if a single subunit performs the molecular function, annotate the gene product to this function without any qualifier, but using relation 'enables (Protein2GO) or enabled by (Noctua)'.<br />
* If the gene product forms homomultimers, also annotate the gene product to this function without any qualifier.<br />
<br />
'''Examples'''<br />
Annotate the catalytic subunit, ''without'' the contributes_to qualifier. <br />
<br />
* '''eIF2''': has three subunits (alpha, beta, gamma); one binds GTP; one binds RNA; the whole complex binds the ribosome (all three subunits are required for ribosome binding). So one subunit is annotated to GTP binding and one to RNA binding without qualifiers, and all three stand in the contributes_to relationship to "ribosome binding". The molecular function annotations should have the extension 'occurs_in' eIF2 complex (GO:0005850), and all three are part_of the cellular component eIF2 complex (GO:0005850). <br />
** '''eIF2gamma''' is the actual GTPase, and eIF2alpha and -beta serving accessory functions. Therefore, eIF2gamma is annotated to GTPase activity; the alpha and beta subunits are '''not''' annotated to GTPase activity [https://www.ncbi.nlm.nih.gov/pubmed/29425030]<br />
<br />
* [http://amigo.geneontology.org/amigo/gene_product/UniProtKB:E2RG47 '''STT3'''] [https://www.ncbi.nlm.nih.gov/pubmed/PMID:12887896]: "dolichyl-diphosphooligosaccharide-protein glycotransferase activity": although it is a member of a complex, it is the catalytic subunit, so it should be annotated without the "contributes_to" qualifier.<br />
<br />
*'''PIGM-PIGX complex''': The PIGM-PIGX complex catalyzes GO:0000030 mannosyltransferase activity. PIGM is the sole catalytic subunit, and while the accessory PIGX subunit is required for activity, it does not have the activity [https://www.ncbi.nlm.nih.gov/pubmed/15635094]. <br />
** Therefore, only PIGM is annotated to GO:0000030 mannosyltransferase activity, without 'contributes_to'.<br />
<br />
* '''Prkag1 (protein kinase AMP-activated non-catalytic subunit gamma 1) [http://amigo.geneontology.org/amigo/gene_product/RGD:3388 RGD:3388]''': PMID:21399626 shows that the activation loop of the kinase domain is stabilized by the regulatory domain. The paper also shows that the regulatory subunit binds ADP, so it is really the subunit with a regulatory role. <br />
** annotation should be to "GO:0019887 protein kinase regulator activity"; Prkag1 does NOT contribute to "AMP-activated protein kinase activity".<br />
* '''Prkaa1 (protein kinase AMP-activated catalytic subunit alpha 1) [http://amigo.geneontology.org/amigo/gene_product/RGD:3388 RGD:3387]''' is the active subunit; is should be annotated to "AMP-activated protein kinase activity", without the "contributes_to" qualifier.<br />
<br />
==Specific cases==<br />
Other common functions for protein complex members: <br />
<br />
===Regulatory subunits===<br />
* If a gene product has been identified as the regulatory subunit of a complex, annotate to "X regulator activity" (GO:0098772 molecular function regulator or a child). Use 'has input' some 'gene product' to describe which gene product the annotated gene product regulates.<br />
*Need examples.<br />
<br />
===Adaptor subunits===<br />
* If a gene product is shown to bring together either a subunit of the complex with another protein, a substrate, a membrane, etc., this gene product may be anotated to GO:0060090 molecular adaptor activity or an appropriate child term.<br />
*Need examples.<br />
<br />
== Quality Control Checks ==<br />
<br />
== Relations Ontology ==<br />
[http://www.ontobee.org/ontology/RO?iri=http://purl.obolibrary.org/obo/RO_0002326 contributes to]<br />
<br />
*if and only if exists c', p' c part_of c' and c' capable_of p and c capable_of p' and p' part_of p then c contributes_to p [RO]<br />
<br />
== Review Status ==<br />
Last reviewed: January 30, 2020<br />
<br />
[http://wiki.geneontology.org/index.php/Annotation_Relations Back to: Annotation Relations]<br />
<br />
[[Category: Gene Product to Term Relations]]</div>Hla28https://wiki.geneontology.org/index.php?title=Contributes_to&diff=78281Contributes to2020-06-09T10:51:15Z<p>Hla28: /* Usage guidance */</p>
<hr />
<div><br />
== Definition ==<br />
A gene product is associated with a GO Molecular Function term using the qualifier 'contributes_to' when it is a member of a complex that is defined as an irreducible molecular machine' - where a particular Molecular Function cannot be ascribed to an individual subunit(s) of a complex.<br />
<br />
== Range ==<br />
The 'contributes_to' qualifier can only be used with GO Molecular Function terms.<br />
<br />
== Child Terms ==<br />
None<br />
<br />
==Usage guidance==<br />
* The 'contributes_to' qualifier is used only in cases where a gene product does not perform a molecular function on its own, but as part of an irreducible molecular machine where the molecular function cannot be attributed to a subunit or group of subunits. Being part of a complex is not sufficient to use this qualifier. <br />
* In all cases, all intrinsic members of a complex should be annotated to 'part of' some 'GO:0032991 protein-containing complex' or an appropriate child term.<br />
<br />
<hr><br />
<br />
===Multiple subunits required for a molecular function===<br />
* All subunits of the to the irreducible molecular machine should be assigned the activity using the 'contributes_to' qualifier. <br />
* For example, if a gene product is part of a complex but only has the function as part of that complex, e.g. forms a composite catalytic site that is required for the function, annotate to the molecular function using the qualifier 'contributes_to'. <br />
<br />
'''Examples'''<br />
<br />
1. '''ATP citrate lyase (ACL) in Chlorobaculum tepidum ''': a heterotetrameric enzyme composed of two distinct subunits, with residues from both subunits comprising the active site. Neither of the subunits expressed alone has ACL activity, but co-expression results in ACL activity. Both subunits contribute_to the ATP citrate lyase activity. '''Annotation for ATP citrate lyase subunit 1:'''<br />
Object: UniProt:Q8KDG1 (CT1089) <br />
Relation: contributes_to<br />
GO term: GO:0003878 ATP citrate synthase activity<br />
Evidence code: IDA<br />
PMID:16952946<br />
<br />
<br />
2. '''Subunits of nuclear RNA polymerases:''' none of the individual subunits have RNA polymerase activity, yet all of these subunits contribute_to DNA-dependent RNA polymerase activity. Note that there are gene products that are members of a nuclear RNA polymerase complex that serve other functions besides the polymerase activity. In these cases, the subunits would not be annotated to polymerase activity using the 'contributes to' qualifier. '''Annotation for ''S. pombe'' RNA polymerase II large subunit Rpb1:'''<br />
<br />
Object: SPBC28F2.12<br />
Relation: contributes_to<br />
GO term: GO:0001055 RNA polymerase II activity<br />
Evidence code: EXP<br />
PMID:9325316<br />
<br />
3. '''MBF transcription factor complex''': res2 and cdc10 are both members of the Schizosaccharomyces pombe MBF transcription factor complex. Each contains, by sequence analysis, a predicted DNA-binding domain. In vitro assays, however, show that neither subunit binds DNA alone; DNA-binding activity is only detectable when the subunits are co-expressed. In this case, res2 and cdc10 are both annotated to GO:0000978 ‘RNA polymerase II cis-regulatory region sequence-specific DNA binding ’ using the ‘contributes to’ qualifier. '''Annotation for res2 MBF complex subunit:'''<br />
Object: PomBase:SPAC22F3.09c (res2)<br />
Relation: contributes_to<br />
GO term: GO:0000978 RNA polymerase II cis-regulatory region sequence-specific DNA binding <br />
Evidence code: IDA<br />
PMID:7926774<br />
<br />
<hr><br />
<br />
===Multi-subunit complex in which the subunit necessary to perform the molecular function is not (yet) known===<br />
<br />
* If a gene product is part of a complex and it is unknown which subunit is responsible for the activity of the complex, annotate all gene products to the molecular function using the qualifier 'contributes_to'. <br />
*Need examples.<br />
<br />
<hr><br />
<br />
===When NOT to use 'contributes_to': single subunit required for a molecular function===<br />
* Being part of a complex does not mean that the molecular function necessarily requires multiple subunits: if a single subunit performs the molecular function, annotate the gene product to this function without any qualifier, but using relation 'enables (Protein2GO) or enabled by (Noctua)'.<br />
* If the gene product forms homomultimers, also annotate the gene product to this function without any qualifier.<br />
<br />
'''Examples'''<br />
Annotate the catalytic subunit, ''without'' the contributes_to qualifier. <br />
<br />
* '''eIF2''': has three subunits (alpha, beta, gamma); one binds GTP; one binds RNA; the whole complex binds the ribosome (all three subunits are required for ribosome binding). So one subunit is annotated to GTP binding and one to RNA binding without qualifiers, and all three stand in the contributes_to relationship to "ribosome binding". The molecular function annotations should have the extension 'occurs_in' eIF2 complex (GO:0005850), and all three are part_of the cellular component eIF2 complex (GO:0005850). <br />
** '''eIF2gamma''' is the actual GTPase, and eIF2alpha and -beta serving accessory functions. Therefore, eIF2gamma is annotated to GTPase activity; the alpha and beta subunits are '''not''' annotated to GTPase activity [https://www.ncbi.nlm.nih.gov/pubmed/29425030]<br />
<br />
* [http://amigo.geneontology.org/amigo/gene_product/UniProtKB:E2RG47 '''STT3'''] [https://www.ncbi.nlm.nih.gov/pubmed/PMID:12887896]: "dolichyl-diphosphooligosaccharide-protein glycotransferase activity": although it is a member of a complex, it is the catalytic subunit, so it should be annotated without the "contributes_to" qualifier.<br />
<br />
*'''PIGM-PIGX complex''': The PIGM-PIGX complex catalyzes GO:0000030 mannosyltransferase activity. PIGM is the sole catalytic subunit, and while the accessory PIGX subunit is required for activity, it does not have the activity [https://www.ncbi.nlm.nih.gov/pubmed/15635094]. <br />
** Therefore, only PIGM is annotated to GO:0000030 mannosyltransferase activity, without 'contributes_to'.<br />
<br />
* '''Prkag1 (protein kinase AMP-activated non-catalytic subunit gamma 1) [http://amigo.geneontology.org/amigo/gene_product/RGD:3388 RGD:3388]''': PMID:21399626 shows that the activation loop of the kinase domain is stabilized by the regulatory domain. The paper also shows that the regulatory subunit binds ADP, so it is really the subunit with a regulatory role. <br />
** annotation should be to "GO:0019887 protein kinase regulator activity"; Prkag1 does NOT contribute to "AMP-activated protein kinase activity".<br />
* '''Prkaa1 (protein kinase AMP-activated catalytic subunit alpha 1) [http://amigo.geneontology.org/amigo/gene_product/RGD:3388 RGD:3387]''' is the active subunit; is should be annotated to "AMP-activated protein kinase activity", without the "contributes_to" qualifier.<br />
<br />
==Specific cases==<br />
Other common functions for protein complex members: <br />
<br />
===Regulatory subunits===<br />
* If a gene product has been identified as the regulatory subunit of a complex, annotate to "X regulator activity" (GO:0098772 molecular function regulator or a child). Use 'has input' some 'gene product' to describe which gene product the annotated gene product regulates.<br />
*Need examples.<br />
<br />
===Adaptor subunits===<br />
* If a gene product is shown to bring together either a subunit of the complex with another protein, a substrate, a membrane, etc., this gene product may be anotated to GO:0060090 molecular adaptor activity or an appropriate child term.<br />
*Need examples.<br />
<br />
== Quality Control Checks ==<br />
<br />
== Relations Ontology ==<br />
[http://www.ontobee.org/ontology/RO?iri=http://purl.obolibrary.org/obo/RO_0002326 contributes to]<br />
<br />
*if and only if exists c', p' c part_of c' and c' capable_of p and c capable_of p' and p' part_of p then c contributes_to p [RO]<br />
<br />
== Review Status ==<br />
Last reviewed: January 30, 2020<br />
<br />
[http://wiki.geneontology.org/index.php/Annotation_Relations Back to: Annotation Relations]<br />
<br />
[[Category: Gene Product to Term Relations]]</div>Hla28https://wiki.geneontology.org/index.php?title=Contributes_to&diff=78280Contributes to2020-06-09T10:07:24Z<p>Hla28: /* Usage guidance */</p>
<hr />
<div><br />
== Definition ==<br />
A gene product is associated with a GO Molecular Function term using the qualifier 'contributes_to' when it is a member of a complex that is defined as an irreducible molecular machine' - where a particular Molecular Function cannot be ascribed to an individual subunit(s) of a complex.<br />
<br />
== Range ==<br />
The 'contributes_to' qualifier can only be used with GO Molecular Function terms.<br />
<br />
== Child Terms ==<br />
None<br />
<br />
==Usage guidance==<br />
* The 'contributes_to' qualifier is used only in cases where a gene product does not perform a molecular function on its own. Being part of a complex is not sufficient to use this qualifier. <br />
* In all cases, all intrinsic members of a complex should be annotated to 'part of' some 'GO:0032991 protein-containing complex' or an appropriate child term.<br />
<br />
<hr><br />
<br />
===Multiple subunits required for a molecular function===<br />
* If multiple subunits participate in the molecular function, annotate all participating subunits to the activity using the 'contributes_to' qualifier. <br />
* For example, if a gene product is part of a complex but only has the function as part of that complex, e.g. forms a composite binding site that is required for the function, annotate to the molecular function using the qualifier 'contributes_to'. <br />
<br />
'''Examples'''<br />
<br />
1. '''ATP citrate lyase (ACL) in Arabidopsis''': it is a heterooctamer, composed of two types of subunits, ACLA and ACLB in a A(4)B(4) stoichiometry. Neither of the subunits expressed alone give ACL activity, but co-expression results in ACL activity. Both subunits contribute_to the ATP citrate lyase activity. '''Annotation for ATP citrate lyase subunit 1:'''<br />
Object: UniProt:Q8KDG1 (CT1089) <br />
Relation: contributes_to<br />
GO term: GO:0003878 ATP citrate synthase activity<br />
Evidence code: IDA<br />
PMID:16952946<br />
<br />
<br />
2. '''Subunits of nuclear RNA polymerases:''' none of the individual subunits have RNA polymerase activity, yet all of these subunits contribute_to DNA-dependent RNA polymerase activity. Note that there are gene products that are members of a nuclear RNA polymerase complex that serve other functions besides the polymerase activity. In these cases, the subunits would not be annotated to polymerase activity using the 'contributes to' qualifier. '''Annotation for ''S. pombe'' RNA polymerase II large subunit Rpb1:'''<br />
<br />
Object: SPBC28F2.12<br />
Relation: contributes_to<br />
GO term: GO:0001055 RNA polymerase II activity<br />
Evidence code: EXP<br />
PMID:9325316<br />
<br />
3. '''MBF transcription factor complex''': res2 and cdc10 are both members of the Schizosaccharomyces pombe MBF transcription factor complex. Each contains, by sequence analysis, a predicted DNA-binding domain. In vitro assays, however, show that neither subunit binds DNA alone; DNA-binding activity is only detectable when the subunits are co-expressed. In this case, res2 and cdc10 are both annotated to GO:0000978 ‘RNA polymerase II cis-regulatory region sequence-specific DNA binding ’ using the ‘contributes to’ qualifier. '''Annotation for res2 MBF complex subunit:'''<br />
Object: PomBase:SPAC22F3.09c (res2)<br />
Relation: contributes_to<br />
GO term: GO:0000978 RNA polymerase II cis-regulatory region sequence-specific DNA binding <br />
Evidence code: IDA<br />
PMID:7926774<br />
<br />
<hr><br />
<br />
===Multi-subunit complex in which the subunit necessary to perform the molecular function is not (yet) known===<br />
<br />
* If a gene product is part of a complex and it is unknown which subunit is responsible for the activity of the complex, annotate all gene products to the molecular function using the qualifier 'contributes_to'. <br />
*Need examples.<br />
<br />
<hr><br />
<br />
===When NOT to use 'contributes_to': single subunit required for a molecular function===<br />
* Being part of a complex does not mean that the molecular function necessarily requires multiple subunits: if a single subunit performs the molecular function, annotate the gene product to this function without any qualifier, but using relation 'enables (Protein2GO) or enabled by (Noctua)'.<br />
* If the gene product forms homomultimers, also annotate the gene product to this function without any qualifier.<br />
<br />
'''Examples'''<br />
Annotate the catalytic subunit, ''without'' the contributes_to qualifier. <br />
<br />
* '''eIF2''': has three subunits (alpha, beta, gamma); one binds GTP; one binds RNA; the whole complex binds the ribosome (all three subunits are required for ribosome binding). So one subunit is annotated to GTP binding and one to RNA binding without qualifiers, and all three stand in the contributes_to relationship to "ribosome binding". The molecular function annotations should have the extension 'occurs_in' eIF2 complex (GO:0005850), and all three are part_of the cellular component eIF2 complex (GO:0005850). <br />
** '''eIF2gamma''' is the actual GTPase, and eIF2alpha and -beta serving accessory functions. Therefore, eIF2gamma is annotated to GTPase activity; the alpha and beta subunits are '''not''' annotated to GTPase activity [https://www.ncbi.nlm.nih.gov/pubmed/29425030]<br />
<br />
* [http://amigo.geneontology.org/amigo/gene_product/UniProtKB:E2RG47 '''STT3'''] [https://www.ncbi.nlm.nih.gov/pubmed/PMID:12887896]: "dolichyl-diphosphooligosaccharide-protein glycotransferase activity": although it is a member of a complex, it is the catalytic subunit, so it should be annotated without the "contributes_to" qualifier.<br />
<br />
*'''PIGM-PIGX complex''': The PIGM-PIGX complex catalyzes GO:0000030 mannosyltransferase activity. PIGM is the sole catalytic subunit, and while the accessory PIGX subunit is required for activity, it does not have the activity [https://www.ncbi.nlm.nih.gov/pubmed/15635094]. <br />
** Therefore, only PIGM is annotated to GO:0000030 mannosyltransferase activity, without 'contributes_to'.<br />
<br />
* '''Prkag1 (protein kinase AMP-activated non-catalytic subunit gamma 1) [http://amigo.geneontology.org/amigo/gene_product/RGD:3388 RGD:3388]''': PMID:21399626 shows that the activation loop of the kinase domain is stabilized by the regulatory domain. The paper also shows that the regulatory subunit binds ADP, so it is really the subunit with a regulatory role. <br />
** annotation should be to "GO:0019887 protein kinase regulator activity"; Prkag1 does NOT contribute to "AMP-activated protein kinase activity".<br />
* '''Prkaa1 (protein kinase AMP-activated catalytic subunit alpha 1) [http://amigo.geneontology.org/amigo/gene_product/RGD:3388 RGD:3387]''' is the active subunit; is should be annotated to "AMP-activated protein kinase activity", without the "contributes_to" qualifier.<br />
<br />
==Specific cases==<br />
Other common functions for protein complex members: <br />
<br />
===Regulatory subunits===<br />
* If a gene product has been identified as the regulatory subunit of a complex, annotate to "X regulator activity" (GO:0098772 molecular function regulator or a child). Use 'has input' some 'gene product' to describe which gene product the annotated gene product regulates.<br />
*Need examples.<br />
<br />
===Adaptor subunits===<br />
* If a gene product is shown to bring together either a subunit of the complex with another protein, a substrate, a membrane, etc., this gene product may be anotated to GO:0060090 molecular adaptor activity or an appropriate child term.<br />
*Need examples.<br />
<br />
== Quality Control Checks ==<br />
<br />
== Relations Ontology ==<br />
[http://www.ontobee.org/ontology/RO?iri=http://purl.obolibrary.org/obo/RO_0002326 contributes to]<br />
<br />
*if and only if exists c', p' c part_of c' and c' capable_of p and c capable_of p' and p' part_of p then c contributes_to p [RO]<br />
<br />
== Review Status ==<br />
Last reviewed: January 30, 2020<br />
<br />
[http://wiki.geneontology.org/index.php/Annotation_Relations Back to: Annotation Relations]<br />
<br />
[[Category: Gene Product to Term Relations]]</div>Hla28https://wiki.geneontology.org/index.php?title=Contributes_to&diff=78279Contributes to2020-06-09T10:06:44Z<p>Hla28: /* Definition */</p>
<hr />
<div><br />
== Definition ==<br />
A gene product is associated with a GO Molecular Function term using the qualifier 'contributes_to' when it is a member of a complex that is defined as an irreducible molecular machine' - where a particular Molecular Function cannot be ascribed to an individual subunit(s) of a complex.<br />
<br />
== Range ==<br />
The 'contributes_to' qualifier can only be used with GO Molecular Function terms.<br />
<br />
== Child Terms ==<br />
None<br />
<br />
==Usage guidance==<br />
* The 'contributes_to' qualifier is used only in cases where a gene product does not perform a molecular function on its own. Being part of a complex is not sufficient to use this qualifier. <br />
* The molecular function annotation for any member of a stable complex should have the extension 'occurs_in' 'GO:0032991 protein-containing complex' or an appropriate child term. <br />
* In all cases, all intrinsic members of a complex should be annotated to 'part of' some 'GO:0032991 protein-containing complex' or an appropriate child term.<br />
<br />
<hr><br />
<br />
===Multiple subunits required for a molecular function===<br />
* If multiple subunits participate in the molecular function, annotate all participating subunits to the activity using the 'contributes_to' qualifier. <br />
* For example, if a gene product is part of a complex but only has the function as part of that complex, e.g. forms a composite binding site that is required for the function, annotate to the molecular function using the qualifier 'contributes_to'. <br />
<br />
'''Examples'''<br />
<br />
1. '''ATP citrate lyase (ACL) in Arabidopsis''': it is a heterooctamer, composed of two types of subunits, ACLA and ACLB in a A(4)B(4) stoichiometry. Neither of the subunits expressed alone give ACL activity, but co-expression results in ACL activity. Both subunits contribute_to the ATP citrate lyase activity. '''Annotation for ATP citrate lyase subunit 1:'''<br />
Object: UniProt:Q8KDG1 (CT1089) <br />
Relation: contributes_to<br />
GO term: GO:0003878 ATP citrate synthase activity<br />
Evidence code: IDA<br />
PMID:16952946<br />
<br />
<br />
2. '''Subunits of nuclear RNA polymerases:''' none of the individual subunits have RNA polymerase activity, yet all of these subunits contribute_to DNA-dependent RNA polymerase activity. Note that there are gene products that are members of a nuclear RNA polymerase complex that serve other functions besides the polymerase activity. In these cases, the subunits would not be annotated to polymerase activity using the 'contributes to' qualifier. '''Annotation for ''S. pombe'' RNA polymerase II large subunit Rpb1:'''<br />
<br />
Object: SPBC28F2.12<br />
Relation: contributes_to<br />
GO term: GO:0001055 RNA polymerase II activity<br />
Evidence code: EXP<br />
PMID:9325316<br />
<br />
3. '''MBF transcription factor complex''': res2 and cdc10 are both members of the Schizosaccharomyces pombe MBF transcription factor complex. Each contains, by sequence analysis, a predicted DNA-binding domain. In vitro assays, however, show that neither subunit binds DNA alone; DNA-binding activity is only detectable when the subunits are co-expressed. In this case, res2 and cdc10 are both annotated to GO:0000978 ‘RNA polymerase II cis-regulatory region sequence-specific DNA binding ’ using the ‘contributes to’ qualifier. '''Annotation for res2 MBF complex subunit:'''<br />
Object: PomBase:SPAC22F3.09c (res2)<br />
Relation: contributes_to<br />
GO term: GO:0000978 RNA polymerase II cis-regulatory region sequence-specific DNA binding <br />
Evidence code: IDA<br />
PMID:7926774<br />
<br />
<hr><br />
<br />
===Multi-subunit complex in which the subunit necessary to perform the molecular function is not (yet) known===<br />
<br />
* If a gene product is part of a complex and it is unknown which subunit is responsible for the activity of the complex, annotate all gene products to the molecular function using the qualifier 'contributes_to'. <br />
*Need examples.<br />
<br />
<hr><br />
<br />
===When NOT to use 'contributes_to': single subunit required for a molecular function===<br />
* Being part of a complex does not mean that the molecular function necessarily requires multiple subunits: if a single subunit performs the molecular function, annotate the gene product to this function without any qualifier, but using relation 'enables (Protein2GO) or enabled by (Noctua)'.<br />
* If the gene product forms homomultimers, also annotate the gene product to this function without any qualifier.<br />
<br />
'''Examples'''<br />
Annotate the catalytic subunit, ''without'' the contributes_to qualifier. <br />
<br />
* '''eIF2''': has three subunits (alpha, beta, gamma); one binds GTP; one binds RNA; the whole complex binds the ribosome (all three subunits are required for ribosome binding). So one subunit is annotated to GTP binding and one to RNA binding without qualifiers, and all three stand in the contributes_to relationship to "ribosome binding". The molecular function annotations should have the extension 'occurs_in' eIF2 complex (GO:0005850), and all three are part_of the cellular component eIF2 complex (GO:0005850). <br />
** '''eIF2gamma''' is the actual GTPase, and eIF2alpha and -beta serving accessory functions. Therefore, eIF2gamma is annotated to GTPase activity; the alpha and beta subunits are '''not''' annotated to GTPase activity [https://www.ncbi.nlm.nih.gov/pubmed/29425030]<br />
<br />
* [http://amigo.geneontology.org/amigo/gene_product/UniProtKB:E2RG47 '''STT3'''] [https://www.ncbi.nlm.nih.gov/pubmed/PMID:12887896]: "dolichyl-diphosphooligosaccharide-protein glycotransferase activity": although it is a member of a complex, it is the catalytic subunit, so it should be annotated without the "contributes_to" qualifier.<br />
<br />
*'''PIGM-PIGX complex''': The PIGM-PIGX complex catalyzes GO:0000030 mannosyltransferase activity. PIGM is the sole catalytic subunit, and while the accessory PIGX subunit is required for activity, it does not have the activity [https://www.ncbi.nlm.nih.gov/pubmed/15635094]. <br />
** Therefore, only PIGM is annotated to GO:0000030 mannosyltransferase activity, without 'contributes_to'.<br />
<br />
* '''Prkag1 (protein kinase AMP-activated non-catalytic subunit gamma 1) [http://amigo.geneontology.org/amigo/gene_product/RGD:3388 RGD:3388]''': PMID:21399626 shows that the activation loop of the kinase domain is stabilized by the regulatory domain. The paper also shows that the regulatory subunit binds ADP, so it is really the subunit with a regulatory role. <br />
** annotation should be to "GO:0019887 protein kinase regulator activity"; Prkag1 does NOT contribute to "AMP-activated protein kinase activity".<br />
* '''Prkaa1 (protein kinase AMP-activated catalytic subunit alpha 1) [http://amigo.geneontology.org/amigo/gene_product/RGD:3388 RGD:3387]''' is the active subunit; is should be annotated to "AMP-activated protein kinase activity", without the "contributes_to" qualifier.<br />
<br />
==Specific cases==<br />
Other common functions for protein complex members: <br />
<br />
===Regulatory subunits===<br />
* If a gene product has been identified as the regulatory subunit of a complex, annotate to "X regulator activity" (GO:0098772 molecular function regulator or a child). Use 'has input' some 'gene product' to describe which gene product the annotated gene product regulates.<br />
*Need examples.<br />
<br />
===Adaptor subunits===<br />
* If a gene product is shown to bring together either a subunit of the complex with another protein, a substrate, a membrane, etc., this gene product may be anotated to GO:0060090 molecular adaptor activity or an appropriate child term.<br />
*Need examples.<br />
<br />
== Quality Control Checks ==<br />
<br />
== Relations Ontology ==<br />
[http://www.ontobee.org/ontology/RO?iri=http://purl.obolibrary.org/obo/RO_0002326 contributes to]<br />
<br />
*if and only if exists c', p' c part_of c' and c' capable_of p and c capable_of p' and p' part_of p then c contributes_to p [RO]<br />
<br />
== Review Status ==<br />
Last reviewed: January 30, 2020<br />
<br />
[http://wiki.geneontology.org/index.php/Annotation_Relations Back to: Annotation Relations]<br />
<br />
[[Category: Gene Product to Term Relations]]</div>Hla28https://wiki.geneontology.org/index.php?title=Annotation_Conf._Call_2020-05-05&diff=78145Annotation Conf. Call 2020-05-052020-05-05T15:04:04Z<p>Hla28: /* Attendance */</p>
<hr />
<div>= Agenda and Minutes =<br />
<br />
== GOC Meeting - May 2020 ==<br />
* Paris consortium meeting scheduled for May 12th - 14th will be held virtually<br />
* We are planning for four hours each day to accommodate the different time zones<br />
* [https://docs.google.com/document/d/1DTBCxib8aRwyw5IWLbYRHtPLCnmcbjUNAV1gwj_2hlo Agenda]<br />
* Users meeting - May 11th<br />
** [http://wiki.geneontology.org/index.php/2020_Remote_GO_Users_Meeting_Logistics Register for users meeting]<br />
<br />
= Attendance =<br />
* On call: Birgit, Bob, Colin, David, Edith, Giulia, Harold, Helen, Kimberly, Laurent-Philippe, Li, Midori, Pascale, Patrick, Petra, Sabrina, Seth, Stacia, Tanya<br />
<br />
[[Category:Annotation Working Group]]</div>Hla28https://wiki.geneontology.org/index.php?title=2020_Paris_GOC_Meeting_Logistics&diff=775332020 Paris GOC Meeting Logistics2020-02-24T08:02:40Z<p>Hla28: /* Attendees */</p>
<hr />
<div>=GOC Meeting, Paris , May 12th - 14th, 2020=<br />
<br />
<span style="color:red">THIS DOCUMENT IS A DRAFT - FINAL VERSION WILL BE ANNOUNCED SOON</span><br />
<br />
==Location==<br />
* [https://research.pasteur.fr/en/network/institut-pasteur-paris-france/#location Pasteur Institute], [https://goo.gl/maps/x5M9YR7Z3urQ8rLM9 28 Rue du Dr Roux] - Lwoff Building - Retrovirus Room.<br />
* Entrance / Security checkin and access to Retrovirus Room: [https://drive.google.com/open?id=1rinBeOdfCaQhChDNfrJOzPWSEYTsXUuS 2D view] [https://drive.google.com/open?id=1XsqfBYeZjVUUHi-zp8HomPk15pGtvREO 3D view]<br />
* '''Be sure to have your current valid ID as it will be required to enter the institute''' !<br />
<br />
==Registration==<br />
* Fee: <span style="color:red">TBD</span> with dinner, or <span style="color:red">TBD</span> for the meeting only<br />
* '''Deadline:''' Friday March 6th, or until full (max 50 people)<br />
<br />
==GO Users Meeting==<br />
* There will be a GO Users meeting Monday May 11. The aim of the meeting is to present GO and discuss with local groups. <br />
<br />
<br />
==Consortium dinner==<br />
* <span style="color:red">May 13</span><br />
<br />
<br />
==Hotels==<br />
<br />
<br />
===Hotel Aberotel (recommended by Pasteur, 8mn walk) ===<br />
24 rue Blomet, 75015 Paris<br />
<br />
Email: aberotel@wanadoo.fr<br />
<br />
Phone: +33 1 40 61 70 50<br />
<br />
[https://www.aberotelparishotel.com website]<br />
<br />
<br />
===Hotel Eiffel Blomet (more modern, 12mn walk)===<br />
78 Rue Blomet, 75015 Paris, France<br />
<br />
Email: info@hoteleiffelblomet.com<br />
<br />
Phone: +33 1 53 68 70 00<br />
<br />
[https://www.hoteleiffelblomet.com website]<br />
<br />
<br />
===Hotel Concorde Montparnasse (13mn walk)===<br />
40 rue du Commandant René Mouchotte, 75014 Paris<br />
<br />
Email: reception@hotel-montparnasse.com<br />
<br />
Phone: +33 1 56 54 84 00<br />
<br />
[http://www.hotel-montparnasse.com/ website]<br />
<br />
<br />
===Hotel Louison (13mn walk)===<br />
105 rue de Vaugirard, 75006 Paris<br />
<br />
Phone: +33 1 53 63 25 50<br />
<br />
Email: welcome@louisonhotel.com<br />
<br />
[https://www.louison-hotel.com/fr website]<br />
<br />
<br />
===Hotel L'aiglon (24mn walk) ===<br />
232 bd Raspail, 75014 Paris<br />
<br />
Email: aiglon@espritdefrance.com<br />
<br />
Phone: +33 1 43 20 82 42<br />
<br />
[http://www.paris-hotel-aiglon.com/ website]<br />
<br />
<br />
==Notes on Hotels==<br />
There are a number of pretty nice apartments in Paris, so if you have time, checking [https://www.airbnb.com/s/Paris--Île-de-France--France/homes?adults=1&children=0&checkin=2020-05-12&checkout=2020-05-14&source=mc_search_bar&place_id=ChIJD7fiBh9u5kcRYJSMaMOCCwQ&click_referer=t%3ASEE_ALL%7Csid%3A9d4e0e3d-0997-4655-808c-570feaaaf297%7Cst%3ALANDING_PAGE_MARQUEE&title_type=NONE&refinement_paths%5B%5D=%2Fhomes AirBnb] could find you a gem for the same price.<br />
<br />
If you don't mind taking the metro (2 stations on line 6 from Edgard Quinet to Pasteur), [https://www.hotelsaintebeuve.com Hotel Sainte-Beuve] is also very nice and closer to the center of Paris and [https://en.wikipedia.org/wiki/Jardin_du_Luxembourg Jardin du Luxembourg]<br />
<br />
==Getting around==<br />
<br />
===Airports===<br />
From Charles de Gaulles Airport, you can go to Paris through:<br />
* [https://www.parisaeroport.fr/en/passengers/access/paris-charles-de-gaulle/public-transport public transport] and the "RER B" line or "le bus direct"<br />
* [https://www.parisaeroport.fr/en/passengers/access/paris-charles-de-gaulle/taxi/paris-cdg-taxi Taxi] for 50 / 55 euros<br />
<br />
===Public transport===<br />
Public transport (RATP) is usually very good in Paris and can get you pretty much everywhere: [https://www.ratp.fr/sites/default/files/plans-lignes/Plans-essentiels/Plan-Metro.1571994565.pdf Downloadable Map]. Metro are mostly to travel within Paris and RER, faster trains can get you to the suburban, including [https://parisbytrain.com/paris-to-chateau-versailles-by-train/ Versailles] (~ 1h).<br />
<br />
The station to get to the meeting is "Pasteur" (south west) and is deserved by both line 6 and 12. <br />
<br />
If you want more precise / up-to-date itineraries than google map, you can use the [RATP site https://www.ratp.fr/en/itineraires].<br />
<br />
===Taxi===<br />
Official Paris Taxi are easily recognizable thanks to their [https://media.timeout.com/images/100013459/1372/772/image.jpg sign], a green light indicating they are available and will stop if you call them. <br />
<br />
===Shared ride===<br />
Uber is available in Paris but not Lyft.<br />
<br />
===Bicycle===<br />
Paris also has a number of biking stations called [https://www.velib-metropole.fr/en/map#/ velib'].<br />
<br />
==Local activities==<br />
The Institut Pasteur is very close to the "Quartier Latin", a very lively part of Paris which concentrate most universities and engineering schools. The [https://en.wikipedia.org/wiki/Rue_Mouffetard rue Mouffetard] and the [https://www.google.com/maps/@48.8444538,2.3492678,3a,75y,77.02h,91.34t/data=!3m7!1e1!3m5!1sevihytHn5fwm5b4jKwbj-A!2e0!6s%2F%2Fgeo3.ggpht.com%2Fcbk%3Fpanoid%3DevihytHn5fwm5b4jKwbj-A%26output%3Dthumbnail%26cb_client%3Dsearch.revgeo_and_fetch.gps%26thumb%3D2%26w%3D96%26h%3D64%26yaw%3D24.475828%26pitch%3D0%26thumbfov%3D100!7i16384!8i8192 Place de la Contrescarpe] are typical of a Paris student life and hold many restaurants. <br />
<br />
This [https://www.discoverwalks.com/blog/10-things-to-see-in-the-latin-quarter/ article] gives some ideas of what can be seen in the area. In 25mn walk you can get to the Gardens of Luxembourg, 35mn will get you to the medieval museum of Cluny, 45mn to the island of the city with Notre Dame cathedral and the Sainte Chapelle (many classical concerts are usually available). If you prefer to use public transportation, taking the line 12 from Pasteur and line 4 from Montparnasse will get you to Saint Michel Notre Dame in 20mn. <br />
<br />
Walking along the Seine river around that area and by a sunny day is always enjoyable. Along the way, it's easy to find the Louvres, the City town hall (Hotel de Ville), the Orsay museum and the [https://www.cometoparis.com/paris-guide/paris-monuments/pont-des-arts-s959 Pont des arts] which leads to the [https://en.wikipedia.org/wiki/Institut_de_France Institut de France] where the French Academy of Science is.<br />
<br />
A one hour tour of Paris by boat is also possible on the [https://www.bateaux-mouches.fr/en/reservation/tickets bateaux mouches] for 14 euros and can be boarded at [https://goo.gl/maps/GkZn4SfyZPjmgLws9 Pont de l'Alma].<br />
<br />
<br />
==Attendees==<br />
Please add yourself to the table if you plan to attend! (If you don't have edit permission, we will soon provide a form to fill out)<br />
Don't forget to register and pay via <span style="color:red">Eventbrite / TBD</span>.<br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Name<br />
! Organization?<br />
! GOC meeting (May 12-14)<br />
! GOC dinner (May 13)<br />
! Users Meeting (May 11)<br />
! Hotel<br />
! Paid via Eventbrite<br />
|-<br />
| Chris Mungall<br />
| LBL<br />
|<br />
|<br />
|<br />
| <br />
| <br />
|-<br />
| Seth Carbon<br />
| LBL<br />
|<br />
|<br />
|<br />
| <br />
|<br />
|-<br />
| Eric Douglass<br />
| LBL<br />
|<br />
|<br />
|<br />
| <br />
|<br />
|-<br />
| Ben Good<br />
| LBL<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|-<br />
| Jim Balhoff<br />
| RENCI<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|-<br />
| Deepak Unni<br />
| LBL<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|-<br />
| Paul Thomas<br />
| USC<br />
|<br />
|<br />
|<br />
| <br />
|<br />
|-<br />
| Huaiyu Mi<br />
| USC<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|-<br />
| Laurent-Philippe Albou<br />
| USC, LBNL<br />
| yes<br />
| yes<br />
| yes<br />
| N/A<br />
| N/A<br />
|-<br />
| Dustin Ebert<br />
| USC<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|-<br />
| Tremayne Mushayahama<br />
| USC<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|-<br />
| Anushya Muruganujan<br />
| USC<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|-<br />
| Pascale Gaudet<br />
| SIB/GOC<br />
| yes<br />
| yes<br />
| possibly<br />
|<br />
|<br />
|-<br />
| Alan Bridge<br />
| SIB/Swiss-Prot/UniProt<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|-<br />
|Petra Fey<br />
|dictyBase<br />
|yes<br />
|yes<br />
| <br />
|<br />
|-<br />
|Suzi Aleksander<br />
|SGD<br />
|yes<br />
|yes<br />
|likely<br />
| <br />
| <br />
|-<br />
|Alexander Diehl<br />
|University at Buffalo<br />
|yes<br />
|yes<br />
|<br />
|<br />
|<br />
|-<br />
|Penelope Garmiri<br />
|EMBL-EBI, GOA<br />
|yes<br />
|yes<br />
|<br />
|<br />
|<br />
|-<br />
|Alex Ignatchenko<br />
|EMBL-EBI, GOA<br />
|yes<br />
|yes<br />
|<br />
|<br />
|<br />
|-<br />
|Maria Martin<br />
|EMBL-EBI, UniProt<br />
|yes<br />
|yes<br />
|<br />
|<br />
|<br />
|-<br />
|Rizwan Ishtiaq<br />
|EMBL-EBI, GOA<br />
|yes<br />
|yes<br />
|<br />
|<br />
|<br />
|-<br />
|David Hill<br />
|MGI/GOC<br />
|yes<br />
|yes<br />
|yes<br />
|<br />
|<br />
|-<br />
|Anne Morgat<br />
|SIB<br />
|yes<br />
|yes<br />
|<br />
|<br />
|<br />
|-<br />
|Marc Feuermann<br />
|SIB<br />
|yes<br />
|yes<br />
|<br />
|<br />
|<br />
|-<br />
|Patrick Masson<br />
|SIB<br />
|yes<br />
|yes<br />
|<br />
|<br />
|<br />
|-<br />
|Helen Attrill<br />
|FlyBase<br />
|yes<br />
|yes<br />
|<br />
|<br />
|<br />
|}<br />
<br />
'''NOT attending (please indicate if you will attend remotely):'''<br/><br />
<br />
<br />
Remote attendees can join us via Zoom (Zoom link will be sent out before the meeting)<br />
<br />
<br />
<br />
<br />
[[Category: GO Consortium Meetings]]</div>Hla28https://wiki.geneontology.org/index.php?title=Progress_Reports&diff=76841Progress Reports2019-11-22T10:26:36Z<p>Hla28: /* Grant Progress Reports */</p>
<hr />
<div>This page gathers links to all progress reports generated for the GO project, including monthly reports from each management group, reports prepared for GO Consortium meetings, and annual reports prepared for the NIH grant. The collection of publications, tutorials, etc. is also linked at the bottom of the page.<br />
<br />
=Grant Progress Reports=<br />
*[https://drive.google.com/drive/folders/1Bv-7MIGpSzXxa7F6CkbhfKzoAcusydGs Grant Progress report 2019]<br />
*[https://drive.google.com/drive/folders/1qoT_E4R_rrkEpDwjqtyfvqrgt66v5Xp9 Grant Progress report 2018]<br />
*[[Grant_Progress_reports_2017]] / [https://drive.google.com/drive/folders/1gPwgQvRsJMEkahF55-bpm0WxJQ5Wfrqh Grant Progress Reports 2017 - Google drive]<br />
*[[Grant_Progress_reports_2016]] / [https://drive.google.com/drive/folders/0B8kRPmmvPJU3SzNuZ0YzVVJEOWc Grant Progress Reports 2016 - Google drive]<br />
*[[Grant_Progress_Reports_2015]]<br />
*[[Grant_Progress_Reports_2014]]<br />
*[[Grant_Progress_Reports_December_2013]]<br />
*[[Grant_Progress_Reports_December_2012]]<br />
*[[Grant_Progress_Reports_December_2010]]<br />
*[[Grant_Progress_Reports_December_2009]]<br />
*[[Grant_Progress_Reports_December_2008]]<br />
*[[Grant_Progress_Reports_2007]]<br />
<br />
=Monthly Managers' Progress Reports=<br />
==User Advocacy & Annotation Outreach==<br />
*[[Annotation_Outreach_group_reports]]<br />
*[[Annotation_Advocacy_Roadmap]]<br />
<br />
==Ontology Development==<br />
*[[Ontology_Development_reports|Ontology Development report list]]<br />
*[[2011_Timeline|Ontology Development Timeline]]<br />
<br />
==Reference Genomes==<br />
*[[Reference_Genome_Progress_Reports]]<br />
*[[Reference_Genome_Timeline]]<br />
<br />
==Software & Utilities==<br />
*[[Software_and_Utilities#Reports|Software and Utilities group reports]]<br />
*[[OBO-Edit_Development_Monthly_Reports|OBO-Edit Development reports]]<br />
*[[SWUG_Timeline_2010-2011|Timeline2010-2011]]<br />
<br />
=GOC Meeting Progress Reports=<br />
*[[Consortium_Meetings#Progress_Reports|Meeting progress report links on meetings page]]<br />
**[[Meeting_Progress_Reports_November_2011]]<br />
**[[Meeting_Progress_Reports_May_2011]]<br />
**[[Meeting_Progress_Reports_March_2010]]<br />
**[[Meeting_Progress_Reports_September_2009|Meeting Progress Reports September 2009]]<br />
**[[Meeting_Progress_Reports_March_2009|Meeting Progress Reports March-April 2009]]<br />
**[[Meeting_Progress_Reports_October_2008]] (collection of links to individual reports)<br />
**[[Meeting_Progress_Report_April_2008]] (one big report page)<br />
*[[Consortium_Meetings#Progress_Report_Templates|Meeting progress report templates]]<br />
<br />
=Publications, tutorials, talks, posters=<br />
*[[Publications, tutorials, talks, posters]]<br />
<br />
[[Category:Reports]]</div>Hla28https://wiki.geneontology.org/index.php?title=Annotation_Conf._Call_2019-09-10&diff=76170Annotation Conf. Call 2019-09-102019-09-10T15:47:04Z<p>Hla28: /* Minutes */</p>
<hr />
<div>= Agenda =<br />
<br />
== October GOC Meeting - Berkeley ==<br />
* [http://wiki.geneontology.org/index.php/2019_Berkeley_GOC_Meeting_Logistics Logistics and Sign-Up]<br />
<br />
== Pipeline ==<br />
* There have been some glitches with the GOC pipeline.<br />
* New ontology terms may not be available for use yet.<br />
* Software team is aware of the issues and working on restoring the pipeline to its regular schedule.<br />
<br />
== Guidelines: github annotation review tickets ==<br />
*Group contacts are listed as 'assignees'<br />
*Please remove your name from the assignee list when you are finished<br />
*Some tickets also have lists or tables listing each group - good to add info here, too, but assignee list is most important<br />
<br />
== GO-CAMs and Annotation Extensions ==<br />
* After USC hackathon in June, we formed a small working group to fully articulate the [https://github.com/geneontology/go-shapes/blob/master/shapes/go-cam-shapes.shex GO-CAM model specifications]<br />
* This will allow for consistent GO-CAM curation using Noctua workbenches, import projects (e.g. Reactome and MOD imports)<br />
* Will also allow us to move forward with harmonizing AE relations used in GO-CAM and conventional annotation<br />
** On today's call, we will review the annotation extension relations that need further discussion, starting with happens_during<br />
** [https://docs.google.com/spreadsheets/d/1zB8UKtG3JRGMkHgXmMpby-K5RFmYxGGRMEXULCCtcPo/edit#gid=1539887761 Google summary spreadsheet of MF extensions]<br />
<br />
=== happens_during ===<br />
* [https://docs.google.com/spreadsheets/d/1qoxnXM3q59jcZLIxnX5SY0H5syfK7GJc38s0VGxx2jM/edit#gid=0 Google spreadsheet for happens during ]<br />
* Current recommendations are that 'happens during' is used to define a biological phase or life stage during which a molecular function occurs<br />
* However, happens_during is not defined in the [https://www.ebi.ac.uk/ols/ontologies/ro/properties?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FRO_0002092 relations ontology]<br />
* There is a comment, however:<br />
** X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y))<br />
** This implies that the start and end of the molecular function and phase are known<br />
** For things like cell cycle phases or development stages this seems fairly straightforward<br />
* But what about annotations that referred to a function that 'happens during' a biological process, such as 'response to oxidative stress'?<br />
* What do we mean when we make these statements?<br />
** WB had seven MF annotations with 'happens during' extensions that needed review.<br />
*** One used a WBls term, so that was okay.<br />
*** The remaining six used 'response to' terms and in reviewing them, I changed the extension relation to 'part of' the 'response to' term. The MFs were all transcription-related functions that mediated the transcriptional response to unfolded protein, or hypoxia, or heat.<br />
** (Pascale): If we want to allow happens_during for 'response to' terms, then we should treat them as 'biological phases', and disallow direct annotations. Are there cases where using 'part_of' versus 'happens_during' makes sense ?<br />
* Updated documentation on 'happens during' usage: http://wiki.geneontology.org/index.php/Annotation_Extension_Relation:happens_during<br />
<br />
== Ontology Updates and Annotation Reviews ==<br />
=== Cellular Component ===<br />
* 'cell part' and child terms<br />
** creation of new term ' cellular anatomical entity'<br />
=== Protein multimerization terms ===<br />
* How are the reviews going?<br />
* Next terms up: protein homodimerization, protein heterodimerization (non-IPI evidence codes)<br />
<br />
=== Transcription terms ===<br />
* Any issues or questions here?<br />
<br />
= Minutes =<br />
*Present: Colin, David, Dmitry, Dustin, Edith, Giulia, Helen, Harold, Karen, Kimberly, Laurent-Philippe, Michelle, Midori, Pascale, Sabrina, Seth, Stacia, Tanya<br />
[[Category:Annotation Working Group]]</div>Hla28https://wiki.geneontology.org/index.php?title=2019_Berkeley_GOC_Meeting_Logistics&diff=760922019 Berkeley GOC Meeting Logistics2019-09-04T08:00:30Z<p>Hla28: /* Attendees */</p>
<hr />
<div>=GOC Meeting, Berkeley, October 7-10, 2019=<br />
<br />
* Location: [https://goo.gl/maps/cfabKMyCSPZmFkFf7| 717 Potter Street, Berkeley, CA]<br />
<br />
==Registration==<br />
* Via [https://www.eventbrite.com/e/2019-goc-berkeley-tickets-68218159351| Eventbrite]--pay online with credit or debit card or Paypal<br />
* $130 registration fee covers coffee & snacks for the 2.5-day GOC meeting, as well as 2 lunches and the Consortium dinner on Oct 9 (not including alcoholic beverages)<br />
* Please also fill in the fields in the Attendees list at the bottom of this page. If you don't have edit permission, you can instead fill out [https://bit.ly/2019GOBerkeley this signup form].<br />
<br />
==Overall schedule== <br />
*Monday, October 7: User Meeting (8:30am-5pm)<br />
*Tuesday-Thursday October 8-10: GOC Meeting (8:30am-5pm first 2 days, 9am-12:30pm third day)<br />
*Friday, October 11 (time TBA): [http://wiki.geneontology.org/index.php/2019_Berkeley_SAB_Meeting_Logistics| SAB Meeting], UC Berkeley campus (Stanley Hall). (SAB dinner will be Thursday, Oct 10)<br />
<br />
==Consortium dinner==<br />
* Wednesday, Oct 9, 6pm, in Berkeley<br />
* More details coming soon<br />
<br />
=User Meeting=<br />
* Monday, October 7 at the same location as the main meeting (717 Potter St., Berkeley). More details soon.<br />
<br />
=SAB Meeting=<br />
* SAB Meeting: Friday, October 11 (time TBA) in Stanley Hall on the UC Berkeley campus. Logistics [http://wiki.geneontology.org/index.php/2019_Berkeley_SAB_Meeting_Logistics| here].<br />
* SAB dinner: Thursday, October 10, 7pm: place TBD<br />
<br />
=Arriving=<br />
<br />
The closest airports are San Francisco (SFO) and Oakland (OAK). From either of those, you can take BART to Berkeley and get a taxi/Lyft/Uber from the Ashby BART station.<br />
<br />
Scroll down to the "Getting around" section for more info.<br />
<br />
=Hotels=<br />
These are listed in increasing order by price. The Four Points by Sheraton is the only one that's walking distance (1.4 miles) from the meeting location; the others are downtown, a short drive away. [https://docs.google.com/document/d/1DaSiBXlW6gjH840h9kdC3FVbuVuetqglcsgrDvB7maE/edit| This map] shows the relative locations of the hotels.<br />
<br />
For travel to our building, we will arrange for attendees to have access to the LBNL Potter St. shuttle to our building from downtown Berkeley.<br />
<br />
===[http://downtownberkeleyinn.com/| Downtown Berkeley Inn]===<br />
* '''Address''': 2001 Bancroft Way, Berkeley (2.4 miles from the meeting location)<br />
* '''Phone''': (510) 843-4043<br />
* '''Rate''': LBNL rate is $129/night (normal rate $139/night).<br />
* '''How to book''': Phone (don't book online) and ask for “LBL” or “Gene Ontology” room block.<br />
** 10 rooms reserved--we may be able to get more if needed.<br />
** Check in as early as Oct 6; check out as late as Oct 12.<br />
** Last day to get the group rate: September 6, 2019.<br />
* '''Description''': Very basic, but adequate.<br />
* '''Advantages''': Cheapest option. Fairly close to downtown Berkeley.<br />
<br />
===[https://www.marriott.com/hotels/travel/sfofp-four-points-san-francisco-bay-bridge/| Four Points by Sheraton Bay Bridge]===<br />
* '''Address''': 1603 Powell Street, Emeryville (1.4 miles from the meeting location),<br />
* '''Phone''': 1-800-325-3535<br />
* '''Rate''': $175/night (single or double) block rate for “Gene Ontology / GO meeting”.<br />
* '''How to book''': Book using this link: https://www.marriott.com/events/start.mi?id=1563407776453&key=GRP or call 1-800-325-3535 and ask for the “Gene Ontology” room block. <br />
** 10 rooms reserved--we may be able to get more if needed.<br />
** Check in as early as Oct 6; check out as late as Oct 12.<br />
** Last day to get the group rate: September 6, 2019.<br />
* '''Description''': A normal hotel. Has an outdoor pool and a fitness center.<br />
* '''Advantages''': Closest hotel to meeting location.<br />
<br />
===[https://www.graduatehotels.com/berkeley/| The Graduate] (formerly the Hotel Durant)===<br />
* '''Address''': 2600 Durant Ave, Berkeley (2.9 miles from the meeting location)<br />
* '''Phone''': 510-845-8981<br />
* '''Rate''': Average of $210/night for a room with one queen.<br />
* '''How to book''': No special rates; you can book [https://www.graduatehotels.com/berkeley| online]<br />
* '''Description''': No pool or fitness center. More distinctive than the similarly-priced Hotel Shattuck Plaza. A recent article about The Graduate noted, "Berkeley's quirky counterculture is represented by bong-shaped lamps in the guestrooms and a restroom urinal painted with the logo and colors of Stanford, Cal-Berkeley’s arch-rival." Known for having made a brief appearance in the movie of the same name.<br />
* '''Advantages''': Near UC Campus and Telegraph Avenue, a colorful if slightly sketchy part of Berkeley.<br />
<br />
===[http://www.hotelshattuckplaza.com| Hotel Shattuck Plaza]===<br />
* '''Address''': 2086 Allston Way, Berkeley (2.5 miles from the meeting location)<br />
* '''Phone''': 866-466-9199<br />
* '''Rate''': UC Berkeley rate: $215/night. Same price for double or single. <br />
* '''How to book''': You will need to phone and ask for the UC Berkeley rate--not available online.<br />
* '''Description''': A more upscale hotel than the previous three, it was completely remodeled a few years ago. Has a fitness center but no pool.<br />
* '''Advantages''': Right in the heart of downtown Berkeley, near BART, Potter St. shuttle, and many world-class restaurants<br />
<br />
= Getting around / To do / Local activities =<br />
<br />
The organizers have lived in the area for a very long time. If you have *any* questions, do not hesitate to reach out to us and let us make your stay in the Bay Area more more pleasant.<br />
<br />
== Getting around ==<br />
<br />
The LBL Potter Street site is located near a highway in a mixed business park and light industrial area.<br />
<br />
=== Walking ===<br />
<br />
Walking from the Emeryville hotel (Four Points Sheraton) to the meeting site is doable, but not necessarily a "pleasant" walk. It takes about half an hour.<br />
<br />
Walking from downtown is not advised and would take about an hour.<br />
<br />
=== By car (inc. "rideshare") ===<br />
<br />
If you are driving to the GO meeting, parking should not be an issue--while there will be no on-site parking, there is usually plenty of on-street parking in the surrounding area if you can walk a little. If you intend on driving, contact Seth or Nomi for details.<br />
<br />
The are usually plenty of Lyfts and Ubers in the area. The downtown area is about 10-12 minutes away.<br />
<br />
=== By public transportation ===<br />
<br />
==== From downtown ====<br />
<br />
===== LBL shuttle =====<br />
<br />
There is a fairly frequent LBL shuttle that directly connects downtown Berkeley area and the Potter Street site:<br />
<br />
https://commute.lbl.gov/resource/shuttle-buses/maps-routes-schedules/potter-st-jbei-route/<br />
<br />
You will need to show an LBL guest pass to board this shuttle. We can provide these on request--contact Seth or Nomi. The shuttle is often a 15-person van, so large groups may need to split up at peak times.<br />
<br />
===== Bus (AC Transit) =====<br />
<br />
There is also a bus that departs from near downtown and the Durant hotel and has a stop quite near the Potter Street site:<br />
<br />
http://www.actransit.org/maps/schedule_results.php?quick_line=36&Go=Go<br />
<br />
==== From Emeryville ====<br />
<br />
While it does not run directly by the hotel, one would need to walk a little and cross a bridge over the tracks, there is a free public shuttle that runs from near the hotel to near the Potter Street site: The Emery Go-round ():<br />
<br />
https://www.emerygoround.com/standard-service.html<br />
<br />
=== Biking and scootering ===<br />
<br />
The are is fairly well served by various "last mile" solutions.<br />
<br />
Rental bikes (now Lyft, previously Ford GoBikes) are available at various locations (https://member.baywheels.com/map/), including downtown Berkeley and near the meeting site (next to the Berkeley Bowl grocery store).<br />
<br />
==Food and drinks==<br />
<br />
=== Overview ===<br />
<br />
Downtown Berkeley has lots of places to eat. The LBL Potter Street location is much more limited for cafes and restaurants, but there is a large supermarket with a cafe (Berkeley Bowl) a few blocks away. Ubereats and the like are always an option for people wanting more variety and many of the organizers will have vehicles and may be doing various errands about town anyways, if there is something in particular you want or need.<br />
<br />
Seth will be happy to talk nearly endlessly about local restaurant, bar, and tea/cafe opportunities.<br />
<br />
==Exercise==<br />
<br />
For people interested in hitting the gym or swimming, the UC Berkeley recreational facilities are open to the general public with day passes:<br />
<br />
https://recsports.berkeley.edu/day-passes/<br />
<br />
The main rec facility and pool location is a short walk from downtown Berkeley. Several of the satellite pools have reduced day pass rates.<br />
<br />
==Things to do in the Berkeley area==<br />
The popular [http://www.hardlystrictlybluegrass.com/2019/ "Hardly Strictly Bluegrass" festival] (which leans more towards alternative rock than bluegrass) will take place in San Francisco, Fri-Sun October 4-6.<br />
<br />
On Wednesday, Oct 8, we will break early for an optional hike in Tilden Park.<br />
<br />
On Thursday, Oct 9, there will be an optional outing to the Exploratorium in San Francisco. The Exploratorium is open [https://www.exploratorium.edu/visit/calendar/after-dark Thursday evenings until 10pm for adults only (18+)]. To add to the fun, we'll take the [https://www.tidelinetickets.com/commute ferry to San Francisco from the Berkeley Marina] and then get dinner near there.<br />
<br />
= Departure = <br />
The GOC meeting will adjourn at 12:30pm on Thursday, October 10; lunch will not be provided (but there are places nearby to buy lunch).<br />
You should allow 1/2 hour to get to Oakland airport by car and 1 hour to get to SFO.<br />
<br />
If you're staying around until Friday, there's an optional expedition on Thursday evening (see above).<br />
<br />
=Attendees=<br />
Please add yourself to the table if you plan to attend! Don't forget to register and pay via [https://www.eventbrite.com/e/2019-goc-berkeley-tickets-68218159351%7C| Eventbrite].<br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Name<br />
! Organization<br />
! GOC meeting (Oct 8-10)?<br />
! GOC dinner (Oct 9)?<br />
! User Meeting (Oct 7)?<br />
! Hotel<br />
! Paid via Eventbrite<br />
|-<br />
| Chris Mungall<br />
| LBL<br />
| Yes<br />
| Yes<br />
| Yes<br />
| N/A<br />
|<br />
|-<br />
| Nomi Harris<br />
| LBL<br />
| Yes<br />
| Yes<br />
| Yes<br />
| N/A<br />
|<br />
|-<br />
| Seth Carbon<br />
| LBL<br />
| Yes<br />
| Yes<br />
| Yes<br />
| N/A<br />
| Yes<br />
|-<br />
| Eric Douglass<br />
| LBL<br />
| Yes<br />
| Yes<br />
| Yes<br />
| N/A<br />
|<br />
|-<br />
| Peter D'Eustachio<br />
| NYULMC / Reactome<br />
| Yes<br />
| Yes<br />
| No<br />
| Four Points<br />
|<br />
|-<br />
| Paul Thomas<br />
| USC<br />
| Yes<br />
| Yes<br />
| Yes<br />
| TBD<br />
|<br />
|-<br />
|Judy Blake<br />
|JAX<br />
|Yes<br />
|Yes<br />
|Yes<br />
|Four Points<br />
|Yes<br />
|-<br />
| Ben Good<br />
| LBL<br />
| Yes<br />
| Yes<br />
| Yes<br />
| Four Points<br />
| Yes<br />
|-<br />
| Jim Balhoff<br />
| RENCI<br />
| Yes<br />
| Yes<br />
| No<br />
| Four Points<br />
| Yes<br />
|-<br />
| Kimberly Van Auken<br />
| WormBase, GO - Caltech<br />
| Yes<br />
| Yes<br />
| Yes<br />
| TBD<br />
| Yes<br />
|-<br />
| David Hill<br />
| MGI, GO - The Jackson Laboratory<br />
| Yes<br />
| No<br />
| Yes<br />
| Four Points<br />
| Yes<br />
|-<br />
| Harold Drabkin<br />
| MGI, GO - The Jackson Laboratory<br />
| Yes<br />
| Yes<br />
| No<br />
| Four Points<br />
| Yes<br />
|-<br />
| Karen Christie<br />
| MGI, GO - The Jackson Laboratory<br />
| Yes<br />
| Yes<br />
| Yes<br />
| Four Points<br />
| Yes<br />
|-<br />
| Laurent-Philippe Albou<br />
| USC, LBNL<br />
| Yes<br />
| Yes<br />
| Yes<br />
| N/A<br />
|<br />
|-<br />
| Edith Wong<br />
| SGD<br />
| Yes<br />
| Yes<br />
| No<br />
| N/A<br />
|<br />
|-<br />
| Tanya Berardini<br />
| TAIR, Phoenix<br />
| Yes<br />
| Yes<br />
| Yes<br />
| N/A<br />
| Yes<br />
|-<br />
| Leonore Reiser<br />
| TAIR, Phoenix<br />
| Fo' sho<br />
| yes<br />
| yes<br />
| N/A<br />
| Yes<br />
|-<br />
| Eva Huala<br />
| TAIR, Phoenix<br />
| Yes<br />
| Yes<br />
| Yes<br />
| N/A<br />
|<br />
|-<br />
| Suzi Aleksander<br />
| SGD, Stanford<br />
| Yes<br />
| Yes<br />
| Yes<br />
| N/A<br />
|<br />
|-<br />
| Mike Cherry<br />
| SGD, Stanford<br />
| Yes<br />
| Yes<br />
| No<br />
| Nash Hotel<br />
| yes<br />
|-<br />
| Huaiyu Mi<br />
| USC<br />
| Yes<br />
| Yes<br />
| Maybe<br />
| Four Points<br />
|<br />
|-<br />
| Ruth Lovering<br />
| UCL<br />
| Yes<br />
| Yes<br />
| Yes<br />
| airbnb<br />
|<br />
|-<br />
| Adam Wright<br />
| OICR<br />
| Yes<br />
| Yes<br />
| Yes<br />
| Hilton Garden Inn<br />
| Yes<br />
|-<br />
| Justin Reese<br />
| LBL<br />
| Yes<br />
| Yes<br />
| Yes<br />
| N/A<br />
| Yes<br />
|-<br />
| Petra Fey<br />
| dictyBase, Northwestern<br />
| Yes<br />
| Yes<br />
| Yes<br />
| not yet booked<br />
|<br />
|-<br />
| Dustin Ebert<br />
| USC<br />
| Yes<br />
| Yes<br />
| Yes<br />
| Oakland airbnb<br />
| Yes<br />
|-<br />
| Pascale Gaudet<br />
| SIB/GOC<br />
| Yes<br />
| Yes<br />
| Yes<br />
| airbnb<br />
| not yet<br />
|-<br />
| Tom Hayman<br />
| RGD<br />
| Yes<br />
| Yes<br />
| Yes<br />
| Four Points<br />
| <br />
|-<br />
| Sabrina Toro<br />
| ZFIN<br />
| Yes<br />
| Yes<br />
| Yes<br />
| TBD<br />
| <br />
|-<br />
| Michelle Giglio<br />
| IGS<br />
| Yes<br />
| Yes<br />
| Yes<br />
| TBD<br />
| not yet<br />
|-<br />
| Suvarna Nadendla<br />
| IGS<br />
| Yes<br />
| Yes<br />
| Yes<br />
| TBD<br />
| not yet<br />
|-<br />
| Alex Ignatchenko<br />
| EBI<br />
| Yes<br />
| Yes<br />
| No<br />
| Hotel Shattuck Plaza<br />
| Yes<br />
|-<br />
| Helen Attrill<br />
| FlyBase<br />
| Yes<br />
| Yes<br />
| No<br />
| Four Points<br />
| Yes<br />
|}<br />
<br />
'''NOT attending (please indicate if you will attend remotely):'''<br/><br />
<br />
Malcolm Fisher (Xenbase) will attend remotely.<br />
<br />
Li Ni (MGI) will attend remotely.<br />
<br />
Birgit Meldal (EBI Complex Portal) - remotely if required (need to see schedule) / manageable (I'm +8 hours)<br />
<br />
Remote attendees can join us via Zoom (Zoom link will be sent out before the meeting)<br />
[[Category: GO Consortium Meetings]]</div>Hla28https://wiki.geneontology.org/index.php?title=2019_Berkeley_GOC_Meeting_Logistics&diff=759072019 Berkeley GOC Meeting Logistics2019-08-09T05:58:11Z<p>Hla28: /* Overall schedule */</p>
<hr />
<div>=GOC Meeting, Berkeley, October 7-10, 2019=<br />
<br />
* Location: [https://goo.gl/maps/cfabKMyCSPZmFkFf7| 717 Potter Street, Berkeley, CA]<br />
<br />
==Registration==<br />
* Via EventBrite--coming soon<br />
* Registration will cover coffee & snacks for the 2.5-day GOC meeting, as well as 2 lunches and the Consortium dinner (not including alcoholic beverages)<br />
<br />
==Overall schedule== <br />
*Monday, October 7: User Meeting (8:30am-5pm)<br />
*Tuesday-Thursday October 8-10: GOC Meeting (8:30am-5pm first 2 days, 9am-12:30pm third day)<br />
*Friday, October 11 (time TBA): SAB Meeting, UC Berkeley campus (Stanley Hall). (SAB dinner will be Thursday, Oct 10)<br />
<br />
==Consortium dinner==<br />
* Wednesday, Oct 9<br />
* More details coming soon<br />
<br />
=User Meeting=<br />
* Monday, October 7 at 717 Potter St., Berkeley. More details soon.<br />
<br />
=SAB Meeting=<br />
* Meeting: Friday, October 11 (time TBA) in Stanley Hall on the UC Berkeley campus. Logistics [http://wiki.geneontology.org/index.php/2019_Berkeley_SAB_Meeting_Logistics| here].<br />
* SAB dinner: Thursday, October 10, 7pm: place TBD<br />
<br />
=Arriving=<br />
<br />
The closest airports are San Francisco (SFO) and Oakland (OAK). From either of those, you can take BART to Berkeley and get a taxi/Lyft/Uber from the Ashby BART station.<br />
<br />
=Hotels=<br />
These are listed in increasing order by price. The Four Points by Sheraton is the only one that's walking distance (1.4 miles) from the meeting location; the others are downtown, a short drive away. [https://docs.google.com/document/d/1DaSiBXlW6gjH840h9kdC3FVbuVuetqglcsgrDvB7maE/edit| This map] shows the relative locations of the hotels.<br />
<br />
For travel to our building, we will arrange for attendees to have access to the LBNL Potter St. shuttle to our building from downtown Berkeley.<br />
<br />
===[http://downtownberkeleyinn.com/| Downtown Berkeley Inn]===<br />
* '''Address''': 2001 Bancroft Way, Berkeley (2.4 miles from the meeting location)<br />
* '''Phone''': (510) 843-4043<br />
* '''Rate''': LBNL rate is $129/night (normal rate $139/night).<br />
* '''How to book''': Phone (don't book online) and ask for “LBL” or “Gene Ontology” room block.<br />
** 10 rooms reserved--we may be able to get more if needed.<br />
** Check in as early as Oct 6; check out as late as Oct 12.<br />
** Last day to get the group rate: September 6, 2019.<br />
* '''Description''': Very basic, but adequate.<br />
* '''Advantages''': Cheapest option. Fairly close to downtown Berkeley.<br />
<br />
===[https://www.marriott.com/hotels/travel/sfofp-four-points-san-francisco-bay-bridge/| Four Points by Sheraton Bay Bridge]===<br />
* '''Address''': 1603 Powell Street, Emeryville (1.4 miles from the meeting location),<br />
* '''Phone''': 1-800-325-3535<br />
* '''Rate''': $175/night (single or double) block rate for “Gene Ontology / GO meeting”.<br />
* '''How to book''': Book using this link: https://www.marriott.com/events/start.mi?id=1563407776453&key=GRP or call 1-800-325-3535 and ask for the “Gene Ontology” room block. <br />
** 10 rooms reserved--we may be able to get more if needed.<br />
** Check in as early as Oct 6; check out as late as Oct 12.<br />
** Last day to get the group rate: September 6, 2019.<br />
* '''Description''': A normal hotel. Has an outdoor pool and a fitness center.<br />
* '''Advantages''': Closest hotel to meeting location.<br />
<br />
===[https://www.graduatehotels.com/berkeley/| The Graduate] (formerly the Hotel Durant)===<br />
* '''Address''': 2600 Durant Ave, Berkeley (2.9 miles from the meeting location)<br />
* '''Phone''': 510-845-8981<br />
* '''Rate''': Average of $210/night for a room with one queen.<br />
* '''How to book''': No special rates; you can book [https://www.graduatehotels.com/berkeley| online]<br />
* '''Description''': No pool or fitness center. More distinctive than the similarly-priced Hotel Shattuck Plaza. A recent article about The Graduate noted, "Berkeley's quirky counterculture is represented by bong-shaped lamps in the guestrooms and a restroom urinal painted with the logo and colors of Stanford, Cal-Berkeley’s arch-rival." Known for having made a brief appearance in the movie of the same name.<br />
* '''Advantages''': Near UC Campus and Telegraph Avenue, a colorful if slightly sketchy part of Berkeley.<br />
<br />
===[http://www.hotelshattuckplaza.com| Hotel Shattuck Plaza]===<br />
* '''Address''': 2086 Allston Way, Berkeley (2.5 miles from the meeting location)<br />
* '''Phone''': 866-466-9199<br />
* '''Rate''': UC Berkeley rate: $215/night. Same price for double or single. <br />
* '''How to book''': You will need to phone and ask for the UC Berkeley rate--not available online.<br />
* '''Description''': A more upscale hotel than the previous three, it was completely remodeled a few years ago. Has a fitness center but no pool.<br />
* '''Advantages''': Right in the heart of downtown Berkeley, near BART, Potter St. shuttle, and many world-class restaurants<br />
<br />
=Attendees=<br />
Please add yourself to the table if you plan to attend!<br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Name<br />
! Organization<br />
! GOC meeting (Oct 8-10)?<br />
! GOC dinner (Oct 9)?<br />
! User Meeting (Oct 7)?<br />
! Hotel<br />
|-<br />
| Chris Mungall<br />
| LBL<br />
| Yes<br />
| Yes<br />
| Yes<br />
| N/A<br />
|-<br />
| Nomi Harris<br />
| LBL<br />
| Yes<br />
| Yes<br />
| Yes<br />
| N/A<br />
|-<br />
| Seth Carbon<br />
| LBL<br />
| Yes<br />
| Yes<br />
| ?<br />
| N/A<br />
|-<br />
| Peter D'Eustachio<br />
| NYULMC / Reactome<br />
| Yes<br />
| Yes<br />
| No<br />
| Four Points<br />
|-<br />
| Paul Thomas<br />
| USC<br />
| Yes<br />
| Yes<br />
| Yes<br />
| TBD<br />
|-<br />
|-<br />
| Ben Good<br />
| LBL<br />
| Yes<br />
| Yes<br />
| Yes<br />
| TBD<br />
|-<br />
|}<br />
<br />
'''NOT attending (please indicate if you will attend remotely):'''<br/><br />
<br />
Remote attendees can join us via Zoom (Zoom link will be sent out before the meeting)<br />
<br />
=Food and drinks=<br />
<br />
= Local activities =<br />
<br />
= Departure = <br />
The GOC meeting will adjourn at 12:30pm on Thursday, October 10; lunch will not be provided (but there are places nearby to buy lunch).<br />
You should allow 1/2 hour to get to Oakland airport by car and 1 hour to get to SFO.<br />
<br />
[[Category: GO Consortium Meetings]]</div>Hla28https://wiki.geneontology.org/index.php?title=2019_Cambridge_GOC_Meeting_Logistics&diff=737382019 Cambridge GOC Meeting Logistics2019-04-05T13:24:19Z<p>Hla28: /* Planned Schedule */</p>
<hr />
<div>=GOC Meeting, Cambridge , April 11th - 12th, 2019=<br />
<br />
* Location: <br />
** [http://www.unicen.cam.ac.uk/ Cambridge University Centre], Hicks Room.<br />
<br />
<br />
==Registration==<br />
* Fee: '''£65''' with dinner, or £35 for the meeting only<br />
* Link to [https://onlinesales.admin.cam.ac.uk/conferences-and-events/biochemistry/go-consortium-meeting/go-consortium-meeting-april-2019 pay by credit or debit card]<br />
* '''Note that this is also the sign-up for dinner on Thursday evening'''<br />
* '''Deadline:''' Thursday March 28th, or until full (max 50 people)<br />
<br />
==Consortium dinner==<br />
7pm Thursday 11th April at [http://www.unicen.cam.ac.uk/riverside-restaurant The Riverside Restaurant], University Centre, Granta Pl, Cambridge CB2 1RU (same venue as the meeting).<br />
<br />
==Planned Schedule== <br />
*8:30am-5pm Thursday April 11th<br />
**8:30-9am Coffee/Tea and check-in <br />
**9am Meeting start<br />
**10:30am Break<br />
**12:30pm Lunch in centre<br />
**3:30pm Break<br />
<br />
<br />
<br />
*7pm Dinner Thursday evening at [http://www.unicen.cam.ac.uk/riverside-restaurant Riverside Restaurant] in the University Centre<br />
<br />
<br />
*9am-5pm Friday April 12th<br />
**8:30-9am Coffee/Tea <br />
**9am Meeting start<br />
**10:30am Break<br />
**12:30pm Lunch in centre<br />
**3:30pm Break<br />
**5pm Meeting end<br />
*Note: 2 days only.<br />
*We'll be running to a pretty tight schedule - many people will have already have been at the Biocurator Conference plus pre-meeting meetings.<br />
<br />
==Meeting Venue and Directions==<br />
* Address Granta Place, Mill Lane, Cambridge, CB2 1RU<br />
** [https://map.cam.ac.uk/University+Centre#52.201128,0.116362,18 Map]<br />
<br />
=Arriving=<br />
<br />
==By Plane==<br />
<br />
(see taxi options from airport in section below)<br />
====Arriving from London Heathrow airport====<br />
<br />
The bus is the cheapest option from Heathrow Airport: there is an hourly bus to Cambridge which leaves from stops at both Heathrow Central Bus Station and Terminal 5. You can check the [http://www.nationalexpress.com/home.aspx National Express website] for timetables and prices. The journey takes around two hours and arrives at [https://www.google.co.uk/maps/place/Parkside,+Cambridge+CB1+1JE/@52.2033603,0.127031,17z/data=!3m1!4b1!4m5!3m4!1s0x47d87090f452bfc3:0x7edb60c4a5b37510!8m2!3d52.203357!4d0.1292197 Parkside, Parker's Piece].<br />
<br />
A faster way to travel would be via taking the London Underground Piccadilly line from the airport to London King's Cross. You can then travel by train from London King's Cross station to Cambridge (the train ticket is approximately £20).<br />
<br />
Another option to reach King's Cross is to take the [https://www.heathrowexpress.com/ Heathrow Express] to Paddington station and change to the London Underground Circle or Hammersmith & City lines. Note that this option is more expensive (around £25, plus £20 for the King's Cross-Cambridge trip) and not much faster than the underground one. If you arrive during the weekend and you book well in advance you may find cheaper tickets for the Heathrow Express service.<br />
<br />
However you reach King's Cross, the trip from there to Cambridge, depending on which train you pick, takes between 50 minutes to 1h and 20 minutes. Add at least 20 minutes to this if you plan to use this occasion to take a picture at Platform 9&#190;, as there will most certainly be a queue!<br />
<br />
You can check trains and times from King's Cross at [http://www.nationalrail.co.uk/default.aspx http://www.nationalrail.co.uk/default.aspx].<br />
<br />
====Arriving from London Stansted airport====<br />
This is the nearest airport to Cambridge, an around 30 minute trip.<br />
Depending on your time of arrival, you will find every half an hour or hourly a direct train to Cambridge, which takes approximately 30 minutes to reach the town. The cost of a one-way ticket is £10. You can check trains and times on [http://www.nationalrail.co.uk/default.aspx http://www.nationalrail.co.uk/default.aspx]. You can also download the [https://www.thetrainline.com/ trainline app] on your phone if you want to get e-tickets directly on your device. Just remember to activate the ticket before going on the train. <br />
<br />
An alternative to the train for arriving in Cambridge from Stansted is via using the National Express coach service. You can check [http://www.nationalexpress.com/home.aspx their website] for times and prices. The airport bus stops at [https://www.google.co.uk/maps/place/Parkside,+Cambridge+CB1+1JE/@52.2033603,0.127031,17z/data=!3m1!4b1!4m5!3m4!1s0x47d87090f452bfc3:0x7edb60c4a5b37510!8m2!3d52.203357!4d0.1292197 Parkside, Parker's Piece].<br />
<br />
====Arriving from London Luton airport====<br />
You can go to the [http://www.nationalexpress.com/home.aspx National Express website] to see timetables and prices of buses from Luton to Cambridge. The ride takes approximately 2 hours. The airport bus stops at [https://www.google.co.uk/maps/place/Parkside,+Cambridge+CB1+1JE/@52.2033603,0.127031,17z/data=!3m1!4b1!4m5!3m4!1s0x47d87090f452bfc3:0x7edb60c4a5b37510!8m2!3d52.203357!4d0.1292197 Parkside, Parker's Piece].<br />
<br />
====Arriving from London Gatwick airport====<br />
The best way to get from London Gatwick airport to Cambridge is to take the train. There is a frequent service from Gatwick to St. Pancras station, which is adjacent to King's Cross station, where you can catch a train to Cambridge. Check train timetables from Luton at [http://www.nationalrail.co.uk/default.aspx http://www.nationalrail.co.uk/default.aspx].<br />
<br />
<br />
'''''N.B. If you arrive at Cambridge via train, you will need your train ticket to exit the station.'''''<br />
<br />
==Taxis==<br />
<br />
If you prefer to reach Cambridge from any airport via a taxi transfer, a company that we can suggest is [http://www.kenwaycars.co.uk/ Kenway]. You can make a booking enquiry through their website or by sending an email to info@kenwaycars.org, specifying airport, flight number, and a destination address.<br />
<br />
If you need a taxi company once in Cambridge, you can use companies like [https://www.panthertaxis.co.uk/ Panther taxi] (01223 715715) or [http://www.camcab.co.uk/ Camcab] (01223 704704). There is Uber in Cambridge, but since the taxis are quite cheap, a Uber ride can often cost the same or more (in rush hours) than a regular taxi ride.<br />
<br />
==From London City Center==<br />
<br />
In case you are going to spend some time in London before coming to Cambridge, you have a few options for coming here.<br />
<br />
====By Train====<br />
<br />
Cambridge is directly connected to London King's Cross and London Liverpool Street. <br />
You can check trains and times at [http://www.nationalrail.co.uk/default.aspx http://www.nationalrail.co.uk/default.aspx] and download the [https://www.thetrainline.com/ trainline app] on your phone if you want to get e-tickets directly on your device.<br />
<br />
'''''N.B. If you arrive at Cambridge via train, you will need your train ticket to exit the station.'''''<br />
<br />
====By Bus====<br />
<br />
Check [http://www.nationalexpress.com/home.aspx National Express website] to see timetables and info. The bus services stop on [https://www.google.co.uk/maps/place/Parkside,+Cambridge+CB1+1JE/@52.2033603,0.127031,17z/data=!3m1!4b1!4m5!3m4!1s0x47d87090f452bfc3:0x7edb60c4a5b37510!8m2!3d52.203357!4d0.1292197 Parkside, Parker's Piece].<br />
<br />
====By Car====<br />
<br />
If you arrive by car a suggestion would be to use the Park and Ride services (details at [http://cambridgeparkandride.info/ http://cambridgeparkandride.info/]), as parking in Cambridge is a nightmare.<br />
<br />
=Attendees=<br />
Please add your name to the table if you intend to attend the meeting and whether you will be booking accommodation (or have booked) at the Double Tree hotel using the discount code, so we can get an estimate.<br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Name<br />
! Organization<br />
! Are you planning to attend the GOC meeting<br />
! I am going to stay at the Double Tree Hotel (Yes/No)<br />
|-<br />
| Seth Carbon<br />
| LBL<br />
| Yes<br />
| No<br />
|-<br />
| Alex Ignatchenko<br />
| EBI (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| Penelope Garmiri<br />
| EBI (Cambridge)<br />
| No<br />
| No<br />
|-<br />
| George Georghiou<br />
| EBI (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| Sandra Orchard<br />
| EBI (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| Maria Martin<br />
| EBI (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| Michele Magrane<br />
| EBI (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| Valerie Wood<br />
| PomBase (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| Giulia Antonazzo<br />
| FlyBase (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| Helen Attrill<br />
| FlyBase (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| Chris Mungall<br />
| LBL<br />
| Yes<br />
| Yes<br />
|-<br />
| Judy Blake<br />
| Jackson Lab<br />
| Yes<br />
| Yes<br />
|-<br />
| Birgit Meldal<br />
| EBI (ComplexPortal / IntAct)<br />
| Yes<br />
| No<br />
|-<br />
| David Hill<br />
| Jackson Lab<br />
| Yes<br />
| Yes<br />
|-<br />
| Harold Drabkin<br />
| Jackson Lab<br />
| Yes<br />
| Yes<br />
|-<br />
| Gaurab Mukherjee<br />
| Jackson Lab<br />
| Yes<br />
| No<br />
|-<br />
| Alan Bridge<br />
| SIB (UniProt / Rhea)<br />
| Yes<br />
| TBC<br />
|-<br />
| Anne Morgat<br />
| SIB (UniProt / Rhea)<br />
| Yes<br />
| TBC<br />
|-<br />
| Lionel Breuza<br />
| SIB (UniProt)<br />
| Yes<br />
| TBC<br />
|-<br />
| Marc Feuermann<br />
| SIB (UniProt)<br />
| Yes<br />
| TBC<br />
|-<br />
| Patrick Masson<br />
| SIB (UniProt / ViralZone)<br />
| Yes<br />
| TBC<br />
|-<br />
|Midori Harris<br />
| PomBase (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
|Huaiyu Mi<br />
| USC<br />
| Yes<br />
| Yes<br />
|-<br />
|Edith Wong<br />
| SGD<br />
| Yes<br />
| No<br />
|-<br />
|Suzi Aleksander<br />
| SGD<br />
| Yes<br />
| No<br />
|-<br />
|Stacia Engel<br />
| SGD<br />
| Yes<br />
| No<br />
|-<br />
|Mike Cherry<br />
| SGD<br />
| Yes<br />
| No<br />
|-<br />
|Felix Gondwe<br />
| SGD<br />
| Yes<br />
| No<br />
|-<br />
|Ruth Lovering<br />
| UCL<br />
| Yes<br />
| No<br />
|-<br />
|Barbara Kramarz<br />
| UCL<br />
| Yes<br />
| No<br />
|-<br />
|Suvarna Nadendla<br />
| ECO (Instit for Genome Sci)<br />
| Yes<br />
| No<br />
|-<br />
|Antonia Lock<br />
| PomBase (Cambridge)<br />
| First day only<br />
| No<br />
|-<br />
|Malcolm Fisher<br />
| Xenbase (CCHMC)<br />
| Yes<br />
| No<br />
|-<br />
|Christina James-Zorn<br />
| Xenbase (CCHMC)<br />
| Yes<br />
| No<br />
|-<br />
|Petra Fey<br />
| dictyBase<br />
| Yes<br />
| TBD<br />
|-<br />
|Sabrina Toro<br />
| ZFIN<br />
| Yes<br />
| No<br />
|-<br />
| Achchuthan Shanmugasundram<br />
| FungiDB<br />
| Yes<br />
|<br />
|-<br />
| Kimberly Van Auken<br />
| WormBase<br />
| Yes<br />
| Yes<br />
|-<br />
| Alayne Cuzick<br />
| PHI-base<br />
| Thursday a.m only<br />
| No <br />
|-<br />
| Paul Sternberg<br />
| WormBase<br />
| Yes<br />
| TBD<br />
|-<br />
| Eric Douglass<br />
| LBL<br />
| Yes<br />
| No<br />
|-<br />
| Eva Huala<br />
| TAIR/Phoenix<br />
| Yes<br />
| No<br />
|-<br />
| Pascale Gaudet<br />
| SIB/USC<br />
| Yes<br />
| TBD<br />
|-<br />
| Paul Thomas<br />
| USC<br />
| Yes<br />
| Yes<br />
|-<br />
| Peter D'Eustachio<br />
| NYUMC / Reactome<br />
| Yes<br />
| Yes<br />
|-<br />
| Laurent-Philippe Albou<br />
| USC<br />
| Yes<br />
| TBD<br />
|-<br />
| Alexander Diehl<br />
| University at Buffalo<br />
| Yes<br />
| Yes<br />
|-<br />
| Nick Brown<br />
| FlyBase<br />
| Yes<br />
| No<br />
|-<br />
| Rob Finn<br />
| InterPro<br />
| Friday p.m. only<br />
| <br />
|-<br />
| Lorne Richardson<br />
| InterPro<br />
| Friday p.m. only<br />
| <br />
|-<br />
| Colin Logie<br />
| Radboud Institute for Molecular Life Sciences<br />
| Thursday only<br />
| TBC<br />
|}<br />
<br />
'''NOT attending (please indicate if you will attend remotely):'''<br/><br />
Nomi Harris (LBNL)--it will be difficult for me to attend remotely due to the 8-hour time difference.<br />
<br/><br />
Mary Dolan (Jackson Lab) will attend remotely<br />
<br/><br />
Tom Hayman (RGD) will attend remotely<br />
<br />
= Group Photo =<br />
<br />
<br />
<br />
=Remote Attendance=<br />
<br />
Please join us via Zoom.<br />
<br />
* https://stanford.zoom.us/j/976175422<br />
<br />
* iPhone one-tap (US Toll): +18333021536,,976175422# or +16507249799,,976175422#<br />
*Telephone:<br />
** +1 650 724 9799 (US, Canada, Caribbean Toll) or +1 833 302 1536 (US, Canada, Caribbean Toll Free).<br />
** UK toll free +44 (0) 80 0031 5717.<br />
** Switzerland toll free +41 800 002 622<br />
<br />
* Meeting ID: 976 175 422<br />
<br />
=Accommodations=<br />
*[http://eventsathilton.com/show/5c38d22f917ce83a55fb2adb BOOK] discounted accommodation at the [https://doubletree3.hilton.com/en/hotels/united-kingdom/doubletree-by-hilton-hotel-cambridge-city-centre-STNCBDI/index.html?WT.mc_id=zELWAKN0EMEA1DT2DMH3LocalSearch4DGGenericx6STNCBDI Double Tree Hotel] for the nights of the 10th-12th April (checkout 13th).<br />
** Address: DoubleTree by Hilton Cambridge City Centre, Granta Place, Mill Lane, Cambridge, CB2 1RT, UK (about 10 seconds from venue, overlooks the river)<br />
**£186.00 per room per night based on single occupancy<br />
**£196.00 per room per night for double occupancy<br />
** Breakfast included (there will be no breakfast provided at the meeting).<br />
<br />
*<b>Discounted booking ends 13th March 2019 and rooms block booking will be released.</b><br />
<br />
<br />
*If you wish to book something else, here are some other options:<br />
**[https://www.accorhotels.com/gb/hotel-8548-ibis-cambridge-central-station/index.shtml Ibis Cambridge Central Station.] 2 Station Square, CB1 2GA Cambrige. Tel: +44 (0) 1223 320960. Prices range from ~£80-£150/night. Approx. 30 minute walk to meeting venue. <br />
**[http://www.thetamburlaine.co.uk/ Tamburlaine Hotel.] 27-29 Station Rd, Cambridge CB1 2FB, UK. Tel: +44 (0) 1223792888. ~£150-240/night. Approx. 30 minute walk to meeting venue.<br />
**[https://www.hotelduvin.com/locations/cambridge/ Hotel du Vin.] 15-19 Trumpington Street, Cambridge CB2 1QA. Tel: +44 (0) 1223 227330. 10 min walk from the meeting venue. Approx. £200/night.<br />
**[https://www.theroyalcambridgehotel.co.uk/ Royal Cambridge Hotel.] Trumpington Street, Cambridge CB2 1PY. Tel: +44 (0)1223 351631. 10 min walk from the meeting venue. email: reservations.cambridge@sjhotels.co.uk. Approx. £160/night.<br />
<br />
=Food and drinks=<br />
<br />
In Cambridge there are many restaurants, of many kinds. In fact, it can get really difficult to pick one! Here are some suggestions, to make your life a bit easier.<br />
*[http://www.themillworks.co.uk/ Millworks]: just across the green from the meeting venue. They define themselves as "an eclectic modern brasserie". You can get good food while being close to the river Cam. Not to be confused with The Mill (see below).<br />
<br />
*[https://www.themillpubcambridge.com/ The Mill]: cosy pub nearly adjacent to the meeting venue, with a good selection of beer and food. Not to be confused with Millworks (see above).<br />
<br />
*[http://www.anchorcambridge.com/ The Anchor]: also close to the meeting venue, serving traditional British pub grub. Pink Floyd had their first gigs in this pub. If you are lucky you can get a table with a nice view over the river.<br />
<br />
*[http://vedanta-cambridge.co.uk/ Vedanta]: very good Indian restaurant on Regent street, but small, so it's good to book in advance!<br />
<br />
*[http://www.thehouseauthenticthai.com/cambridge/home.html The House]: a good and cheap Thai restaurant, again on Regent Street.<br />
<br />
*[http://www.eagle-cambridge.co.uk/ The Eagle]: the pub where Francis Crick announced on February 28th, 1953 that he and James Watson had "discovered the secret of life" (the structure of the DNA).<br />
<br />
*[http://www.aromi.co.uk/ Aromi]: in case you want to have a slice of Italian pizza and a good coffee, maybe together with some Sicilian cannoli or some ice cream. There are two Aromi restaurants in the city centre, very close to each other, and they sell different products. They are both usually very busy!<br />
<br />
*[http://www.sticksnsushi.co.uk/restaurants/cambridge.html Sticks'n'sushi]: Japanese restaurant in the city centre, with nice sushi and a cool atmosphere. A bit on the pricey side.<br />
<br />
*[https://www.iguanas.co.uk/restaurants/cambridge Las Iguanas]: Latin American restaurant on Quayside with a vibrant atmosphere. Always with a 2-for-1 cocktail offer, in case you just want to go there for drinks. It does get a bit noisy with loud music, so not great if you look for something quiet.<br />
<br />
*[https://thaikhun.co.uk/ Thaikhun]: in case you still want to stay in the Quayside area, this is a good Thai restaurant, still with an interesting vibe, but quieter<br />
<br />
*[http://www.sixcambridge.co.uk/ Six]: if the weather is good, you can get a nice view of Cambridge, either from the rooftop bar, or from the restaurant that is on the floor right under the bar (so, unlike the bar, it's covered).<br />
<br />
What constitutes a good coffee is of course really subjective, but here are some suggestions in case you are desperate:<br />
<br />
*[http://www.aromi.co.uk/ Aromi]<br />
*[https://caffenero.com/uk/en/ Caffé Nero]<br />
*[http://www.savinos.co.uk/contactUs.php Savino's]<br />
*[http://www.fitzbillies.com/ Fitzbillies] (also good for an afternoon tea)<br />
*[http://hotnumberscoffee.co.uk/land Hot Numbers] [https://www.google.co.uk/maps/place/Hot+Numbers+Coffee/@52.1992715,0.121472,15z/data=!4m8!1m2!2m1!1sHot+Numbers,+Unit+6+Dale's+Brewery,+Gwydir+Street,+Cambridge,,+,+,+gb!3m4!1s0x47d870988d4c481b:0xc97ca0e02fb73288!8m2!3d52.1984856!4d0.1219986 Map]<br />
*If you prefer, we also have a few [https://www.starbucks.co.uk/store-locator?map=52.204051,0.121294,15z Starbucks] in Cambridge!<br />
<br />
= Local activities =<br />
<br />
<br />
[[Category: GO Consortium Meetings]]</div>Hla28https://wiki.geneontology.org/index.php?title=2019_Cambridge_GOC_Meeting_Logistics&diff=737372019 Cambridge GOC Meeting Logistics2019-04-05T13:24:05Z<p>Hla28: /* Planned Schedule */</p>
<hr />
<div>=GOC Meeting, Cambridge , April 11th - 12th, 2019=<br />
<br />
* Location: <br />
** [http://www.unicen.cam.ac.uk/ Cambridge University Centre], Hicks Room.<br />
<br />
<br />
==Registration==<br />
* Fee: '''£65''' with dinner, or £35 for the meeting only<br />
* Link to [https://onlinesales.admin.cam.ac.uk/conferences-and-events/biochemistry/go-consortium-meeting/go-consortium-meeting-april-2019 pay by credit or debit card]<br />
* '''Note that this is also the sign-up for dinner on Thursday evening'''<br />
* '''Deadline:''' Thursday March 28th, or until full (max 50 people)<br />
<br />
==Consortium dinner==<br />
7pm Thursday 11th April at [http://www.unicen.cam.ac.uk/riverside-restaurant The Riverside Restaurant], University Centre, Granta Pl, Cambridge CB2 1RU (same venue as the meeting).<br />
<br />
==Planned Schedule== <br />
*8:30am-5pm Thursday April 11th<br />
**8:30-9am Coffee/Tea and registration <br />
**9am Meeting start<br />
**10:30am Break<br />
**12:30pm Lunch in centre<br />
**3:30pm Break<br />
<br />
<br />
<br />
*7pm Dinner Thursday evening at [http://www.unicen.cam.ac.uk/riverside-restaurant Riverside Restaurant] in the University Centre<br />
<br />
<br />
*9am-5pm Friday April 12th<br />
**8:30-9am Coffee/Tea <br />
**9am Meeting start<br />
**10:30am Break<br />
**12:30pm Lunch in centre<br />
**3:30pm Break<br />
**5pm Meeting end<br />
*Note: 2 days only.<br />
*We'll be running to a pretty tight schedule - many people will have already have been at the Biocurator Conference plus pre-meeting meetings.<br />
<br />
==Meeting Venue and Directions==<br />
* Address Granta Place, Mill Lane, Cambridge, CB2 1RU<br />
** [https://map.cam.ac.uk/University+Centre#52.201128,0.116362,18 Map]<br />
<br />
=Arriving=<br />
<br />
==By Plane==<br />
<br />
(see taxi options from airport in section below)<br />
====Arriving from London Heathrow airport====<br />
<br />
The bus is the cheapest option from Heathrow Airport: there is an hourly bus to Cambridge which leaves from stops at both Heathrow Central Bus Station and Terminal 5. You can check the [http://www.nationalexpress.com/home.aspx National Express website] for timetables and prices. The journey takes around two hours and arrives at [https://www.google.co.uk/maps/place/Parkside,+Cambridge+CB1+1JE/@52.2033603,0.127031,17z/data=!3m1!4b1!4m5!3m4!1s0x47d87090f452bfc3:0x7edb60c4a5b37510!8m2!3d52.203357!4d0.1292197 Parkside, Parker's Piece].<br />
<br />
A faster way to travel would be via taking the London Underground Piccadilly line from the airport to London King's Cross. You can then travel by train from London King's Cross station to Cambridge (the train ticket is approximately £20).<br />
<br />
Another option to reach King's Cross is to take the [https://www.heathrowexpress.com/ Heathrow Express] to Paddington station and change to the London Underground Circle or Hammersmith & City lines. Note that this option is more expensive (around £25, plus £20 for the King's Cross-Cambridge trip) and not much faster than the underground one. If you arrive during the weekend and you book well in advance you may find cheaper tickets for the Heathrow Express service.<br />
<br />
However you reach King's Cross, the trip from there to Cambridge, depending on which train you pick, takes between 50 minutes to 1h and 20 minutes. Add at least 20 minutes to this if you plan to use this occasion to take a picture at Platform 9&#190;, as there will most certainly be a queue!<br />
<br />
You can check trains and times from King's Cross at [http://www.nationalrail.co.uk/default.aspx http://www.nationalrail.co.uk/default.aspx].<br />
<br />
====Arriving from London Stansted airport====<br />
This is the nearest airport to Cambridge, an around 30 minute trip.<br />
Depending on your time of arrival, you will find every half an hour or hourly a direct train to Cambridge, which takes approximately 30 minutes to reach the town. The cost of a one-way ticket is £10. You can check trains and times on [http://www.nationalrail.co.uk/default.aspx http://www.nationalrail.co.uk/default.aspx]. You can also download the [https://www.thetrainline.com/ trainline app] on your phone if you want to get e-tickets directly on your device. Just remember to activate the ticket before going on the train. <br />
<br />
An alternative to the train for arriving in Cambridge from Stansted is via using the National Express coach service. You can check [http://www.nationalexpress.com/home.aspx their website] for times and prices. The airport bus stops at [https://www.google.co.uk/maps/place/Parkside,+Cambridge+CB1+1JE/@52.2033603,0.127031,17z/data=!3m1!4b1!4m5!3m4!1s0x47d87090f452bfc3:0x7edb60c4a5b37510!8m2!3d52.203357!4d0.1292197 Parkside, Parker's Piece].<br />
<br />
====Arriving from London Luton airport====<br />
You can go to the [http://www.nationalexpress.com/home.aspx National Express website] to see timetables and prices of buses from Luton to Cambridge. The ride takes approximately 2 hours. The airport bus stops at [https://www.google.co.uk/maps/place/Parkside,+Cambridge+CB1+1JE/@52.2033603,0.127031,17z/data=!3m1!4b1!4m5!3m4!1s0x47d87090f452bfc3:0x7edb60c4a5b37510!8m2!3d52.203357!4d0.1292197 Parkside, Parker's Piece].<br />
<br />
====Arriving from London Gatwick airport====<br />
The best way to get from London Gatwick airport to Cambridge is to take the train. There is a frequent service from Gatwick to St. Pancras station, which is adjacent to King's Cross station, where you can catch a train to Cambridge. Check train timetables from Luton at [http://www.nationalrail.co.uk/default.aspx http://www.nationalrail.co.uk/default.aspx].<br />
<br />
<br />
'''''N.B. If you arrive at Cambridge via train, you will need your train ticket to exit the station.'''''<br />
<br />
==Taxis==<br />
<br />
If you prefer to reach Cambridge from any airport via a taxi transfer, a company that we can suggest is [http://www.kenwaycars.co.uk/ Kenway]. You can make a booking enquiry through their website or by sending an email to info@kenwaycars.org, specifying airport, flight number, and a destination address.<br />
<br />
If you need a taxi company once in Cambridge, you can use companies like [https://www.panthertaxis.co.uk/ Panther taxi] (01223 715715) or [http://www.camcab.co.uk/ Camcab] (01223 704704). There is Uber in Cambridge, but since the taxis are quite cheap, a Uber ride can often cost the same or more (in rush hours) than a regular taxi ride.<br />
<br />
==From London City Center==<br />
<br />
In case you are going to spend some time in London before coming to Cambridge, you have a few options for coming here.<br />
<br />
====By Train====<br />
<br />
Cambridge is directly connected to London King's Cross and London Liverpool Street. <br />
You can check trains and times at [http://www.nationalrail.co.uk/default.aspx http://www.nationalrail.co.uk/default.aspx] and download the [https://www.thetrainline.com/ trainline app] on your phone if you want to get e-tickets directly on your device.<br />
<br />
'''''N.B. If you arrive at Cambridge via train, you will need your train ticket to exit the station.'''''<br />
<br />
====By Bus====<br />
<br />
Check [http://www.nationalexpress.com/home.aspx National Express website] to see timetables and info. The bus services stop on [https://www.google.co.uk/maps/place/Parkside,+Cambridge+CB1+1JE/@52.2033603,0.127031,17z/data=!3m1!4b1!4m5!3m4!1s0x47d87090f452bfc3:0x7edb60c4a5b37510!8m2!3d52.203357!4d0.1292197 Parkside, Parker's Piece].<br />
<br />
====By Car====<br />
<br />
If you arrive by car a suggestion would be to use the Park and Ride services (details at [http://cambridgeparkandride.info/ http://cambridgeparkandride.info/]), as parking in Cambridge is a nightmare.<br />
<br />
=Attendees=<br />
Please add your name to the table if you intend to attend the meeting and whether you will be booking accommodation (or have booked) at the Double Tree hotel using the discount code, so we can get an estimate.<br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Name<br />
! Organization<br />
! Are you planning to attend the GOC meeting<br />
! I am going to stay at the Double Tree Hotel (Yes/No)<br />
|-<br />
| Seth Carbon<br />
| LBL<br />
| Yes<br />
| No<br />
|-<br />
| Alex Ignatchenko<br />
| EBI (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| Penelope Garmiri<br />
| EBI (Cambridge)<br />
| No<br />
| No<br />
|-<br />
| George Georghiou<br />
| EBI (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| Sandra Orchard<br />
| EBI (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| Maria Martin<br />
| EBI (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| Michele Magrane<br />
| EBI (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| Valerie Wood<br />
| PomBase (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| Giulia Antonazzo<br />
| FlyBase (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| Helen Attrill<br />
| FlyBase (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| Chris Mungall<br />
| LBL<br />
| Yes<br />
| Yes<br />
|-<br />
| Judy Blake<br />
| Jackson Lab<br />
| Yes<br />
| Yes<br />
|-<br />
| Birgit Meldal<br />
| EBI (ComplexPortal / IntAct)<br />
| Yes<br />
| No<br />
|-<br />
| David Hill<br />
| Jackson Lab<br />
| Yes<br />
| Yes<br />
|-<br />
| Harold Drabkin<br />
| Jackson Lab<br />
| Yes<br />
| Yes<br />
|-<br />
| Gaurab Mukherjee<br />
| Jackson Lab<br />
| Yes<br />
| No<br />
|-<br />
| Alan Bridge<br />
| SIB (UniProt / Rhea)<br />
| Yes<br />
| TBC<br />
|-<br />
| Anne Morgat<br />
| SIB (UniProt / Rhea)<br />
| Yes<br />
| TBC<br />
|-<br />
| Lionel Breuza<br />
| SIB (UniProt)<br />
| Yes<br />
| TBC<br />
|-<br />
| Marc Feuermann<br />
| SIB (UniProt)<br />
| Yes<br />
| TBC<br />
|-<br />
| Patrick Masson<br />
| SIB (UniProt / ViralZone)<br />
| Yes<br />
| TBC<br />
|-<br />
|Midori Harris<br />
| PomBase (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
|Huaiyu Mi<br />
| USC<br />
| Yes<br />
| Yes<br />
|-<br />
|Edith Wong<br />
| SGD<br />
| Yes<br />
| No<br />
|-<br />
|Suzi Aleksander<br />
| SGD<br />
| Yes<br />
| No<br />
|-<br />
|Stacia Engel<br />
| SGD<br />
| Yes<br />
| No<br />
|-<br />
|Mike Cherry<br />
| SGD<br />
| Yes<br />
| No<br />
|-<br />
|Felix Gondwe<br />
| SGD<br />
| Yes<br />
| No<br />
|-<br />
|Ruth Lovering<br />
| UCL<br />
| Yes<br />
| No<br />
|-<br />
|Barbara Kramarz<br />
| UCL<br />
| Yes<br />
| No<br />
|-<br />
|Suvarna Nadendla<br />
| ECO (Instit for Genome Sci)<br />
| Yes<br />
| No<br />
|-<br />
|Antonia Lock<br />
| PomBase (Cambridge)<br />
| First day only<br />
| No<br />
|-<br />
|Malcolm Fisher<br />
| Xenbase (CCHMC)<br />
| Yes<br />
| No<br />
|-<br />
|Christina James-Zorn<br />
| Xenbase (CCHMC)<br />
| Yes<br />
| No<br />
|-<br />
|Petra Fey<br />
| dictyBase<br />
| Yes<br />
| TBD<br />
|-<br />
|Sabrina Toro<br />
| ZFIN<br />
| Yes<br />
| No<br />
|-<br />
| Achchuthan Shanmugasundram<br />
| FungiDB<br />
| Yes<br />
|<br />
|-<br />
| Kimberly Van Auken<br />
| WormBase<br />
| Yes<br />
| Yes<br />
|-<br />
| Alayne Cuzick<br />
| PHI-base<br />
| Thursday a.m only<br />
| No <br />
|-<br />
| Paul Sternberg<br />
| WormBase<br />
| Yes<br />
| TBD<br />
|-<br />
| Eric Douglass<br />
| LBL<br />
| Yes<br />
| No<br />
|-<br />
| Eva Huala<br />
| TAIR/Phoenix<br />
| Yes<br />
| No<br />
|-<br />
| Pascale Gaudet<br />
| SIB/USC<br />
| Yes<br />
| TBD<br />
|-<br />
| Paul Thomas<br />
| USC<br />
| Yes<br />
| Yes<br />
|-<br />
| Peter D'Eustachio<br />
| NYUMC / Reactome<br />
| Yes<br />
| Yes<br />
|-<br />
| Laurent-Philippe Albou<br />
| USC<br />
| Yes<br />
| TBD<br />
|-<br />
| Alexander Diehl<br />
| University at Buffalo<br />
| Yes<br />
| Yes<br />
|-<br />
| Nick Brown<br />
| FlyBase<br />
| Yes<br />
| No<br />
|-<br />
| Rob Finn<br />
| InterPro<br />
| Friday p.m. only<br />
| <br />
|-<br />
| Lorne Richardson<br />
| InterPro<br />
| Friday p.m. only<br />
| <br />
|-<br />
| Colin Logie<br />
| Radboud Institute for Molecular Life Sciences<br />
| Thursday only<br />
| TBC<br />
|}<br />
<br />
'''NOT attending (please indicate if you will attend remotely):'''<br/><br />
Nomi Harris (LBNL)--it will be difficult for me to attend remotely due to the 8-hour time difference.<br />
<br/><br />
Mary Dolan (Jackson Lab) will attend remotely<br />
<br/><br />
Tom Hayman (RGD) will attend remotely<br />
<br />
= Group Photo =<br />
<br />
<br />
<br />
=Remote Attendance=<br />
<br />
Please join us via Zoom.<br />
<br />
* https://stanford.zoom.us/j/976175422<br />
<br />
* iPhone one-tap (US Toll): +18333021536,,976175422# or +16507249799,,976175422#<br />
*Telephone:<br />
** +1 650 724 9799 (US, Canada, Caribbean Toll) or +1 833 302 1536 (US, Canada, Caribbean Toll Free).<br />
** UK toll free +44 (0) 80 0031 5717.<br />
** Switzerland toll free +41 800 002 622<br />
<br />
* Meeting ID: 976 175 422<br />
<br />
=Accommodations=<br />
*[http://eventsathilton.com/show/5c38d22f917ce83a55fb2adb BOOK] discounted accommodation at the [https://doubletree3.hilton.com/en/hotels/united-kingdom/doubletree-by-hilton-hotel-cambridge-city-centre-STNCBDI/index.html?WT.mc_id=zELWAKN0EMEA1DT2DMH3LocalSearch4DGGenericx6STNCBDI Double Tree Hotel] for the nights of the 10th-12th April (checkout 13th).<br />
** Address: DoubleTree by Hilton Cambridge City Centre, Granta Place, Mill Lane, Cambridge, CB2 1RT, UK (about 10 seconds from venue, overlooks the river)<br />
**£186.00 per room per night based on single occupancy<br />
**£196.00 per room per night for double occupancy<br />
** Breakfast included (there will be no breakfast provided at the meeting).<br />
<br />
*<b>Discounted booking ends 13th March 2019 and rooms block booking will be released.</b><br />
<br />
<br />
*If you wish to book something else, here are some other options:<br />
**[https://www.accorhotels.com/gb/hotel-8548-ibis-cambridge-central-station/index.shtml Ibis Cambridge Central Station.] 2 Station Square, CB1 2GA Cambrige. Tel: +44 (0) 1223 320960. Prices range from ~£80-£150/night. Approx. 30 minute walk to meeting venue. <br />
**[http://www.thetamburlaine.co.uk/ Tamburlaine Hotel.] 27-29 Station Rd, Cambridge CB1 2FB, UK. Tel: +44 (0) 1223792888. ~£150-240/night. Approx. 30 minute walk to meeting venue.<br />
**[https://www.hotelduvin.com/locations/cambridge/ Hotel du Vin.] 15-19 Trumpington Street, Cambridge CB2 1QA. Tel: +44 (0) 1223 227330. 10 min walk from the meeting venue. Approx. £200/night.<br />
**[https://www.theroyalcambridgehotel.co.uk/ Royal Cambridge Hotel.] Trumpington Street, Cambridge CB2 1PY. Tel: +44 (0)1223 351631. 10 min walk from the meeting venue. email: reservations.cambridge@sjhotels.co.uk. Approx. £160/night.<br />
<br />
=Food and drinks=<br />
<br />
In Cambridge there are many restaurants, of many kinds. In fact, it can get really difficult to pick one! Here are some suggestions, to make your life a bit easier.<br />
*[http://www.themillworks.co.uk/ Millworks]: just across the green from the meeting venue. They define themselves as "an eclectic modern brasserie". You can get good food while being close to the river Cam. Not to be confused with The Mill (see below).<br />
<br />
*[https://www.themillpubcambridge.com/ The Mill]: cosy pub nearly adjacent to the meeting venue, with a good selection of beer and food. Not to be confused with Millworks (see above).<br />
<br />
*[http://www.anchorcambridge.com/ The Anchor]: also close to the meeting venue, serving traditional British pub grub. Pink Floyd had their first gigs in this pub. If you are lucky you can get a table with a nice view over the river.<br />
<br />
*[http://vedanta-cambridge.co.uk/ Vedanta]: very good Indian restaurant on Regent street, but small, so it's good to book in advance!<br />
<br />
*[http://www.thehouseauthenticthai.com/cambridge/home.html The House]: a good and cheap Thai restaurant, again on Regent Street.<br />
<br />
*[http://www.eagle-cambridge.co.uk/ The Eagle]: the pub where Francis Crick announced on February 28th, 1953 that he and James Watson had "discovered the secret of life" (the structure of the DNA).<br />
<br />
*[http://www.aromi.co.uk/ Aromi]: in case you want to have a slice of Italian pizza and a good coffee, maybe together with some Sicilian cannoli or some ice cream. There are two Aromi restaurants in the city centre, very close to each other, and they sell different products. They are both usually very busy!<br />
<br />
*[http://www.sticksnsushi.co.uk/restaurants/cambridge.html Sticks'n'sushi]: Japanese restaurant in the city centre, with nice sushi and a cool atmosphere. A bit on the pricey side.<br />
<br />
*[https://www.iguanas.co.uk/restaurants/cambridge Las Iguanas]: Latin American restaurant on Quayside with a vibrant atmosphere. Always with a 2-for-1 cocktail offer, in case you just want to go there for drinks. It does get a bit noisy with loud music, so not great if you look for something quiet.<br />
<br />
*[https://thaikhun.co.uk/ Thaikhun]: in case you still want to stay in the Quayside area, this is a good Thai restaurant, still with an interesting vibe, but quieter<br />
<br />
*[http://www.sixcambridge.co.uk/ Six]: if the weather is good, you can get a nice view of Cambridge, either from the rooftop bar, or from the restaurant that is on the floor right under the bar (so, unlike the bar, it's covered).<br />
<br />
What constitutes a good coffee is of course really subjective, but here are some suggestions in case you are desperate:<br />
<br />
*[http://www.aromi.co.uk/ Aromi]<br />
*[https://caffenero.com/uk/en/ Caffé Nero]<br />
*[http://www.savinos.co.uk/contactUs.php Savino's]<br />
*[http://www.fitzbillies.com/ Fitzbillies] (also good for an afternoon tea)<br />
*[http://hotnumberscoffee.co.uk/land Hot Numbers] [https://www.google.co.uk/maps/place/Hot+Numbers+Coffee/@52.1992715,0.121472,15z/data=!4m8!1m2!2m1!1sHot+Numbers,+Unit+6+Dale's+Brewery,+Gwydir+Street,+Cambridge,,+,+,+gb!3m4!1s0x47d870988d4c481b:0xc97ca0e02fb73288!8m2!3d52.1984856!4d0.1219986 Map]<br />
*If you prefer, we also have a few [https://www.starbucks.co.uk/store-locator?map=52.204051,0.121294,15z Starbucks] in Cambridge!<br />
<br />
= Local activities =<br />
<br />
<br />
[[Category: GO Consortium Meetings]]</div>Hla28https://wiki.geneontology.org/index.php?title=2019_Cambridge_GOC_Meeting_Logistics&diff=737352019 Cambridge GOC Meeting Logistics2019-04-05T13:11:03Z<p>Hla28: /* Planned Schedule */</p>
<hr />
<div>=GOC Meeting, Cambridge , April 11th - 12th, 2019=<br />
<br />
* Location: <br />
** [http://www.unicen.cam.ac.uk/ Cambridge University Centre], Hicks Room.<br />
<br />
<br />
==Registration==<br />
* Fee: '''£65''' with dinner, or £35 for the meeting only<br />
* Link to [https://onlinesales.admin.cam.ac.uk/conferences-and-events/biochemistry/go-consortium-meeting/go-consortium-meeting-april-2019 pay by credit or debit card]<br />
* '''Note that this is also the sign-up for dinner on Thursday evening'''<br />
* '''Deadline:''' Thursday March 28th, or until full (max 50 people)<br />
<br />
==Consortium dinner==<br />
7pm Thursday 11th April at [http://www.unicen.cam.ac.uk/riverside-restaurant The Riverside Restaurant], University Centre, Granta Pl, Cambridge CB2 1RU (same venue as the meeting).<br />
<br />
==Planned Schedule== <br />
*8:30am-5pm Thursday April 11th<br />
**8:30-9am Coffee/Tea and registration <br />
**9am Meeting start<br />
**10:30am Break<br />
**12:30pm Lunch in centre<br />
**3:30pm Break<br />
<br />
<br />
<br />
*7pm Dinner Thursday evening at [http://www.unicen.cam.ac.uk/riverside-restaurant Riverside Restaurant] in the University Centre<br />
<br />
<br />
*9am-5pm Friday April 12th<br />
**8:30-9am Coffee/Tea and registration <br />
**9am Meeting start<br />
**10:30am Break<br />
**12:30pm Lunch in centre<br />
**3:30pm Break<br />
**5pm Meeting end<br />
*Note: 2 days only.<br />
*We'll be running to a pretty tight schedule - many people will have already have been at the Biocurator Conference plus pre-meeting meetings.<br />
<br />
==Meeting Venue and Directions==<br />
* Address Granta Place, Mill Lane, Cambridge, CB2 1RU<br />
** [https://map.cam.ac.uk/University+Centre#52.201128,0.116362,18 Map]<br />
<br />
=Arriving=<br />
<br />
==By Plane==<br />
<br />
(see taxi options from airport in section below)<br />
====Arriving from London Heathrow airport====<br />
<br />
The bus is the cheapest option from Heathrow Airport: there is an hourly bus to Cambridge which leaves from stops at both Heathrow Central Bus Station and Terminal 5. You can check the [http://www.nationalexpress.com/home.aspx National Express website] for timetables and prices. The journey takes around two hours and arrives at [https://www.google.co.uk/maps/place/Parkside,+Cambridge+CB1+1JE/@52.2033603,0.127031,17z/data=!3m1!4b1!4m5!3m4!1s0x47d87090f452bfc3:0x7edb60c4a5b37510!8m2!3d52.203357!4d0.1292197 Parkside, Parker's Piece].<br />
<br />
A faster way to travel would be via taking the London Underground Piccadilly line from the airport to London King's Cross. You can then travel by train from London King's Cross station to Cambridge (the train ticket is approximately £20).<br />
<br />
Another option to reach King's Cross is to take the [https://www.heathrowexpress.com/ Heathrow Express] to Paddington station and change to the London Underground Circle or Hammersmith & City lines. Note that this option is more expensive (around £25, plus £20 for the King's Cross-Cambridge trip) and not much faster than the underground one. If you arrive during the weekend and you book well in advance you may find cheaper tickets for the Heathrow Express service.<br />
<br />
However you reach King's Cross, the trip from there to Cambridge, depending on which train you pick, takes between 50 minutes to 1h and 20 minutes. Add at least 20 minutes to this if you plan to use this occasion to take a picture at Platform 9&#190;, as there will most certainly be a queue!<br />
<br />
You can check trains and times from King's Cross at [http://www.nationalrail.co.uk/default.aspx http://www.nationalrail.co.uk/default.aspx].<br />
<br />
====Arriving from London Stansted airport====<br />
This is the nearest airport to Cambridge, an around 30 minute trip.<br />
Depending on your time of arrival, you will find every half an hour or hourly a direct train to Cambridge, which takes approximately 30 minutes to reach the town. The cost of a one-way ticket is £10. You can check trains and times on [http://www.nationalrail.co.uk/default.aspx http://www.nationalrail.co.uk/default.aspx]. You can also download the [https://www.thetrainline.com/ trainline app] on your phone if you want to get e-tickets directly on your device. Just remember to activate the ticket before going on the train. <br />
<br />
An alternative to the train for arriving in Cambridge from Stansted is via using the National Express coach service. You can check [http://www.nationalexpress.com/home.aspx their website] for times and prices. The airport bus stops at [https://www.google.co.uk/maps/place/Parkside,+Cambridge+CB1+1JE/@52.2033603,0.127031,17z/data=!3m1!4b1!4m5!3m4!1s0x47d87090f452bfc3:0x7edb60c4a5b37510!8m2!3d52.203357!4d0.1292197 Parkside, Parker's Piece].<br />
<br />
====Arriving from London Luton airport====<br />
You can go to the [http://www.nationalexpress.com/home.aspx National Express website] to see timetables and prices of buses from Luton to Cambridge. The ride takes approximately 2 hours. The airport bus stops at [https://www.google.co.uk/maps/place/Parkside,+Cambridge+CB1+1JE/@52.2033603,0.127031,17z/data=!3m1!4b1!4m5!3m4!1s0x47d87090f452bfc3:0x7edb60c4a5b37510!8m2!3d52.203357!4d0.1292197 Parkside, Parker's Piece].<br />
<br />
====Arriving from London Gatwick airport====<br />
The best way to get from London Gatwick airport to Cambridge is to take the train. There is a frequent service from Gatwick to St. Pancras station, which is adjacent to King's Cross station, where you can catch a train to Cambridge. Check train timetables from Luton at [http://www.nationalrail.co.uk/default.aspx http://www.nationalrail.co.uk/default.aspx].<br />
<br />
<br />
'''''N.B. If you arrive at Cambridge via train, you will need your train ticket to exit the station.'''''<br />
<br />
==Taxis==<br />
<br />
If you prefer to reach Cambridge from any airport via a taxi transfer, a company that we can suggest is [http://www.kenwaycars.co.uk/ Kenway]. You can make a booking enquiry through their website or by sending an email to info@kenwaycars.org, specifying airport, flight number, and a destination address.<br />
<br />
If you need a taxi company once in Cambridge, you can use companies like [https://www.panthertaxis.co.uk/ Panther taxi] (01223 715715) or [http://www.camcab.co.uk/ Camcab] (01223 704704). There is Uber in Cambridge, but since the taxis are quite cheap, a Uber ride can often cost the same or more (in rush hours) than a regular taxi ride.<br />
<br />
==From London City Center==<br />
<br />
In case you are going to spend some time in London before coming to Cambridge, you have a few options for coming here.<br />
<br />
====By Train====<br />
<br />
Cambridge is directly connected to London King's Cross and London Liverpool Street. <br />
You can check trains and times at [http://www.nationalrail.co.uk/default.aspx http://www.nationalrail.co.uk/default.aspx] and download the [https://www.thetrainline.com/ trainline app] on your phone if you want to get e-tickets directly on your device.<br />
<br />
'''''N.B. If you arrive at Cambridge via train, you will need your train ticket to exit the station.'''''<br />
<br />
====By Bus====<br />
<br />
Check [http://www.nationalexpress.com/home.aspx National Express website] to see timetables and info. The bus services stop on [https://www.google.co.uk/maps/place/Parkside,+Cambridge+CB1+1JE/@52.2033603,0.127031,17z/data=!3m1!4b1!4m5!3m4!1s0x47d87090f452bfc3:0x7edb60c4a5b37510!8m2!3d52.203357!4d0.1292197 Parkside, Parker's Piece].<br />
<br />
====By Car====<br />
<br />
If you arrive by car a suggestion would be to use the Park and Ride services (details at [http://cambridgeparkandride.info/ http://cambridgeparkandride.info/]), as parking in Cambridge is a nightmare.<br />
<br />
=Attendees=<br />
Please add your name to the table if you intend to attend the meeting and whether you will be booking accommodation (or have booked) at the Double Tree hotel using the discount code, so we can get an estimate.<br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Name<br />
! Organization<br />
! Are you planning to attend the GOC meeting<br />
! I am going to stay at the Double Tree Hotel (Yes/No)<br />
|-<br />
| Seth Carbon<br />
| LBL<br />
| Yes<br />
| No<br />
|-<br />
| Alex Ignatchenko<br />
| EBI (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| Penelope Garmiri<br />
| EBI (Cambridge)<br />
| No<br />
| No<br />
|-<br />
| George Georghiou<br />
| EBI (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| Sandra Orchard<br />
| EBI (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| Maria Martin<br />
| EBI (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| Michele Magrane<br />
| EBI (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| Valerie Wood<br />
| PomBase (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| Giulia Antonazzo<br />
| FlyBase (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| Helen Attrill<br />
| FlyBase (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| Chris Mungall<br />
| LBL<br />
| Yes<br />
| Yes<br />
|-<br />
| Judy Blake<br />
| Jackson Lab<br />
| Yes<br />
| Yes<br />
|-<br />
| Birgit Meldal<br />
| EBI (ComplexPortal / IntAct)<br />
| Yes<br />
| No<br />
|-<br />
| David Hill<br />
| Jackson Lab<br />
| Yes<br />
| Yes<br />
|-<br />
| Harold Drabkin<br />
| Jackson Lab<br />
| Yes<br />
| Yes<br />
|-<br />
| Gaurab Mukherjee<br />
| Jackson Lab<br />
| Yes<br />
| No<br />
|-<br />
| Alan Bridge<br />
| SIB (UniProt / Rhea)<br />
| Yes<br />
| TBC<br />
|-<br />
| Anne Morgat<br />
| SIB (UniProt / Rhea)<br />
| Yes<br />
| TBC<br />
|-<br />
| Lionel Breuza<br />
| SIB (UniProt)<br />
| Yes<br />
| TBC<br />
|-<br />
| Marc Feuermann<br />
| SIB (UniProt)<br />
| Yes<br />
| TBC<br />
|-<br />
| Patrick Masson<br />
| SIB (UniProt / ViralZone)<br />
| Yes<br />
| TBC<br />
|-<br />
|Midori Harris<br />
| PomBase (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
|Huaiyu Mi<br />
| USC<br />
| Yes<br />
| Yes<br />
|-<br />
|Edith Wong<br />
| SGD<br />
| Yes<br />
| No<br />
|-<br />
|Suzi Aleksander<br />
| SGD<br />
| Yes<br />
| No<br />
|-<br />
|Stacia Engel<br />
| SGD<br />
| Yes<br />
| No<br />
|-<br />
|Mike Cherry<br />
| SGD<br />
| Yes<br />
| No<br />
|-<br />
|Felix Gondwe<br />
| SGD<br />
| Yes<br />
| No<br />
|-<br />
|Ruth Lovering<br />
| UCL<br />
| Yes<br />
| No<br />
|-<br />
|Barbara Kramarz<br />
| UCL<br />
| Yes<br />
| No<br />
|-<br />
|Suvarna Nadendla<br />
| ECO (Instit for Genome Sci)<br />
| Yes<br />
| No<br />
|-<br />
|Antonia Lock<br />
| PomBase (Cambridge)<br />
| First day only<br />
| No<br />
|-<br />
|Malcolm Fisher<br />
| Xenbase (CCHMC)<br />
| Yes<br />
| No<br />
|-<br />
|Christina James-Zorn<br />
| Xenbase (CCHMC)<br />
| Yes<br />
| No<br />
|-<br />
|Petra Fey<br />
| dictyBase<br />
| Yes<br />
| TBD<br />
|-<br />
|Sabrina Toro<br />
| ZFIN<br />
| Yes<br />
| No<br />
|-<br />
| Achchuthan Shanmugasundram<br />
| FungiDB<br />
| Yes<br />
|<br />
|-<br />
| Kimberly Van Auken<br />
| WormBase<br />
| Yes<br />
| Yes<br />
|-<br />
| Alayne Cuzick<br />
| PHI-base<br />
| Thursday a.m only<br />
| No <br />
|-<br />
| Paul Sternberg<br />
| WormBase<br />
| Yes<br />
| TBD<br />
|-<br />
| Eric Douglass<br />
| LBL<br />
| Yes<br />
| No<br />
|-<br />
| Eva Huala<br />
| TAIR/Phoenix<br />
| Yes<br />
| No<br />
|-<br />
| Pascale Gaudet<br />
| SIB/USC<br />
| Yes<br />
| TBD<br />
|-<br />
| Paul Thomas<br />
| USC<br />
| Yes<br />
| Yes<br />
|-<br />
| Peter D'Eustachio<br />
| NYUMC / Reactome<br />
| Yes<br />
| Yes<br />
|-<br />
| Laurent-Philippe Albou<br />
| USC<br />
| Yes<br />
| TBD<br />
|-<br />
| Alexander Diehl<br />
| University at Buffalo<br />
| Yes<br />
| Yes<br />
|-<br />
| Nick Brown<br />
| FlyBase<br />
| Yes<br />
| No<br />
|-<br />
| Rob Finn<br />
| InterPro<br />
| Friday p.m. only<br />
| <br />
|-<br />
| Lorne Richardson<br />
| InterPro<br />
| Friday p.m. only<br />
| <br />
|-<br />
| Colin Logie<br />
| Radboud Institute for Molecular Life Sciences<br />
| Thursday only<br />
| TBC<br />
|}<br />
<br />
'''NOT attending (please indicate if you will attend remotely):'''<br/><br />
Nomi Harris (LBNL)--it will be difficult for me to attend remotely due to the 8-hour time difference.<br />
<br/><br />
Mary Dolan (Jackson Lab) will attend remotely<br />
<br/><br />
Tom Hayman (RGD) will attend remotely<br />
<br />
= Group Photo =<br />
<br />
<br />
<br />
=Remote Attendance=<br />
<br />
Please join us via Zoom.<br />
<br />
* https://stanford.zoom.us/j/976175422<br />
<br />
* iPhone one-tap (US Toll): +18333021536,,976175422# or +16507249799,,976175422#<br />
*Telephone:<br />
** +1 650 724 9799 (US, Canada, Caribbean Toll) or +1 833 302 1536 (US, Canada, Caribbean Toll Free).<br />
** UK toll free +44 (0) 80 0031 5717.<br />
** Switzerland toll free +41 800 002 622<br />
<br />
* Meeting ID: 976 175 422<br />
<br />
=Accommodations=<br />
*[http://eventsathilton.com/show/5c38d22f917ce83a55fb2adb BOOK] discounted accommodation at the [https://doubletree3.hilton.com/en/hotels/united-kingdom/doubletree-by-hilton-hotel-cambridge-city-centre-STNCBDI/index.html?WT.mc_id=zELWAKN0EMEA1DT2DMH3LocalSearch4DGGenericx6STNCBDI Double Tree Hotel] for the nights of the 10th-12th April (checkout 13th).<br />
** Address: DoubleTree by Hilton Cambridge City Centre, Granta Place, Mill Lane, Cambridge, CB2 1RT, UK (about 10 seconds from venue, overlooks the river)<br />
**£186.00 per room per night based on single occupancy<br />
**£196.00 per room per night for double occupancy<br />
** Breakfast included (there will be no breakfast provided at the meeting).<br />
<br />
*<b>Discounted booking ends 13th March 2019 and rooms block booking will be released.</b><br />
<br />
<br />
*If you wish to book something else, here are some other options:<br />
**[https://www.accorhotels.com/gb/hotel-8548-ibis-cambridge-central-station/index.shtml Ibis Cambridge Central Station.] 2 Station Square, CB1 2GA Cambrige. Tel: +44 (0) 1223 320960. Prices range from ~£80-£150/night. Approx. 30 minute walk to meeting venue. <br />
**[http://www.thetamburlaine.co.uk/ Tamburlaine Hotel.] 27-29 Station Rd, Cambridge CB1 2FB, UK. Tel: +44 (0) 1223792888. ~£150-240/night. Approx. 30 minute walk to meeting venue.<br />
**[https://www.hotelduvin.com/locations/cambridge/ Hotel du Vin.] 15-19 Trumpington Street, Cambridge CB2 1QA. Tel: +44 (0) 1223 227330. 10 min walk from the meeting venue. Approx. £200/night.<br />
**[https://www.theroyalcambridgehotel.co.uk/ Royal Cambridge Hotel.] Trumpington Street, Cambridge CB2 1PY. Tel: +44 (0)1223 351631. 10 min walk from the meeting venue. email: reservations.cambridge@sjhotels.co.uk. Approx. £160/night.<br />
<br />
=Food and drinks=<br />
<br />
In Cambridge there are many restaurants, of many kinds. In fact, it can get really difficult to pick one! Here are some suggestions, to make your life a bit easier.<br />
*[http://www.themillworks.co.uk/ Millworks]: just across the green from the meeting venue. They define themselves as "an eclectic modern brasserie". You can get good food while being close to the river Cam. Not to be confused with The Mill (see below).<br />
<br />
*[https://www.themillpubcambridge.com/ The Mill]: cosy pub nearly adjacent to the meeting venue, with a good selection of beer and food. Not to be confused with Millworks (see above).<br />
<br />
*[http://www.anchorcambridge.com/ The Anchor]: also close to the meeting venue, serving traditional British pub grub. Pink Floyd had their first gigs in this pub. If you are lucky you can get a table with a nice view over the river.<br />
<br />
*[http://vedanta-cambridge.co.uk/ Vedanta]: very good Indian restaurant on Regent street, but small, so it's good to book in advance!<br />
<br />
*[http://www.thehouseauthenticthai.com/cambridge/home.html The House]: a good and cheap Thai restaurant, again on Regent Street.<br />
<br />
*[http://www.eagle-cambridge.co.uk/ The Eagle]: the pub where Francis Crick announced on February 28th, 1953 that he and James Watson had "discovered the secret of life" (the structure of the DNA).<br />
<br />
*[http://www.aromi.co.uk/ Aromi]: in case you want to have a slice of Italian pizza and a good coffee, maybe together with some Sicilian cannoli or some ice cream. There are two Aromi restaurants in the city centre, very close to each other, and they sell different products. They are both usually very busy!<br />
<br />
*[http://www.sticksnsushi.co.uk/restaurants/cambridge.html Sticks'n'sushi]: Japanese restaurant in the city centre, with nice sushi and a cool atmosphere. A bit on the pricey side.<br />
<br />
*[https://www.iguanas.co.uk/restaurants/cambridge Las Iguanas]: Latin American restaurant on Quayside with a vibrant atmosphere. Always with a 2-for-1 cocktail offer, in case you just want to go there for drinks. It does get a bit noisy with loud music, so not great if you look for something quiet.<br />
<br />
*[https://thaikhun.co.uk/ Thaikhun]: in case you still want to stay in the Quayside area, this is a good Thai restaurant, still with an interesting vibe, but quieter<br />
<br />
*[http://www.sixcambridge.co.uk/ Six]: if the weather is good, you can get a nice view of Cambridge, either from the rooftop bar, or from the restaurant that is on the floor right under the bar (so, unlike the bar, it's covered).<br />
<br />
What constitutes a good coffee is of course really subjective, but here are some suggestions in case you are desperate:<br />
<br />
*[http://www.aromi.co.uk/ Aromi]<br />
*[https://caffenero.com/uk/en/ Caffé Nero]<br />
*[http://www.savinos.co.uk/contactUs.php Savino's]<br />
*[http://www.fitzbillies.com/ Fitzbillies] (also good for an afternoon tea)<br />
*[http://hotnumberscoffee.co.uk/land Hot Numbers] [https://www.google.co.uk/maps/place/Hot+Numbers+Coffee/@52.1992715,0.121472,15z/data=!4m8!1m2!2m1!1sHot+Numbers,+Unit+6+Dale's+Brewery,+Gwydir+Street,+Cambridge,,+,+,+gb!3m4!1s0x47d870988d4c481b:0xc97ca0e02fb73288!8m2!3d52.1984856!4d0.1219986 Map]<br />
*If you prefer, we also have a few [https://www.starbucks.co.uk/store-locator?map=52.204051,0.121294,15z Starbucks] in Cambridge!<br />
<br />
= Local activities =<br />
<br />
<br />
[[Category: GO Consortium Meetings]]</div>Hla28