Talk:MiRNA guidelines: Difference between revisions

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|'occurs_in' cell (CL ID) and/or tissue (Uberon ID); ‘has_regulation_target’ mRNA (ENSEMBL transcript ID)
|'occurs_in' cell (CL ID) and/or tissue (Uberon ID); ‘has_regulation_target’ mRNA (ENSEMBL transcript ID)
|-valign="top"
|-valign="top"
|'''6''' evidence in the paper of specific negative or positive regulation of mRNA; if negative/positive regulation of the mRNA is demonstrated but this is a ‘fishing’ experiment and there is no information from the author that the targets are expected to be regulated.  
|'''6a''' evidence in the paper of specific negative or positive regulation of mRNA; if the author explains why the targets are expected to be regulated.  
|GO:0010468 regulation of gene expression, GO:0010629 negative regulation of gene expression, GO:0010628 positive regulation of gene expression
|GO:0010468 regulation of gene expression, GO:0010629 negative regulation of gene expression, GO:0010628 positive regulation of gene expression
|IDA or IMP
|IDA or IMP
|'occurs_in' cell (CL ID) and/or tissue (Uberon ID); ‘has_regulation_target’ mRNA (ENSEMBL transcript ID)
|'occurs_in' cell (CL ID) and/or tissue (Uberon ID); AND include ‘has_regulation_target’ mRNA (ENSEMBL transcript ID)
|-valign="top"
|'''6b''' evidence in the paper of specific negative or positive regulation of mRNA; if negative/positive regulation of the mRNA is demonstrated but this is a ‘fishing’ experiment and there is no information from the author that the targets are expected to be regulated.
|GO:0010468 regulation of gene expression, GO:0010629 negative regulation of gene expression, GO:0010628 positive regulation of gene expression
|IDA or IMP
|'occurs_in' cell (CL ID) and/or tissue (Uberon ID); NO ‘has_regulation_target’
|-valign="top"
|-valign="top"
|'''7''' evidence in the paper of specific negative regulation of mRNA; plus specific mRNA binding demonstrated (this could be in a different paper)
|'''7''' evidence in the paper of specific negative regulation of mRNA; plus specific mRNA binding demonstrated (this could be in a different paper)

Revision as of 07:11, 19 January 2015

back to the agenda page

back to the miRNA agenda page

miRNA Questionnaire questions

all annotations to PMID:22269326

Consortium minutes [1]

pdf of presentation File:GOCmiRNA2014.pdf

General agreement

Attendees: Ruth Lovering, Rachael Huntley, David Hill, Judy Blake, Dmitry Sitnikov, Karen Christie, Pascale Gaudet, Rama Balakrishnan, Tanya Berardini, Donghui Li, Doug Howe, Jennifer Smith, Harold Drabkin

Annotation approach summary table

Experiment GO Term Evidence Code Annotation Extension
1 pre-miR transfection, (usually use IDA although this will be over-expression); No evidence that the cell or tissue used normally express this miR Downstream/upstream Biological Process (application determined by experiment and authors intent) IDA None
2a pre-miR transfection, (usually use IDA although this will be over-expression); Evidence that the cell or tissue normally used express this miR Downstream Biological Process (application determined by experiment and authors intent), for example GO:1901311 regulation of gene expression involved in extracellular matrix organization OR GO:1901311 regulation of gene expression/GO:0035195 gene silencing by miRNA AND annotation extension IDA 'occurs_in' cell (CL ID) and/or tissue (Uberon ID); 'part_of' BP eg: GO:0030198 extracellular matrix organization
2b pre-miR transfection, (usually use IDA although this will be over-expression); Evidence that the cell or tissue normally used express this miR Upstream Biological Process, for example GO:1901311 regulation of gene expression/GO:0035195 gene silencing by miRNA AND Annotation extension IDA 'occurs_in' cell (CL ID) and/or tissue (Uberon ID); ; 'part_of' BP eg: GO:0071560 cellular response to transforming growth factor beta stimulus
3 anti-miR transfection, (knockdown of miR) Downstream and upstream Biological Processes (as above, application determined by experiment and authors intent) IMP 'occurs_in' cell (CL ID) and/or tissue (Uberon ID)
4A evidence in the paper of specific negative regulation of mRNA; plus specific mRNA binding demonstrated (this could be in a different paper) GO:0035195 gene silencing by miRNA IDA or IMP 'occurs_in' cell (CL ID) and/or tissue (Uberon ID); ‘has_direct_input’ mRNA (ENSEMBL transcript ID)
4B (see above for process only that would need to be created for data extraction) evidence in the paper of specific negative regulation of mRNA; plus specific mRNA binding demonstrated (this could be in a different paper) GO:1903231 mRNA binding involved in posttranscriptional gene silencing IDA or IMP 'occurs_in' cell (CL ID) and/or tissue (Uberon ID); ‘has_direct_input’ mRNA (ENSEMBL transcript ID)
5 evidence in the paper of specific negative regulation of mRNA; plus this is the authors intent (ie they suggest that this is an expected target for the miRNA); Recognise that there will be occasions when these annotations are not correct, as the miR may regulate translation of another gene which then regulates translation of the target mRNA. GO:0035195 gene silencing by miRNA IDA or IMP 'occurs_in' cell (CL ID) and/or tissue (Uberon ID); ‘has_regulation_target’ mRNA (ENSEMBL transcript ID)
6a evidence in the paper of specific negative or positive regulation of mRNA; if the author explains why the targets are expected to be regulated. GO:0010468 regulation of gene expression, GO:0010629 negative regulation of gene expression, GO:0010628 positive regulation of gene expression IDA or IMP 'occurs_in' cell (CL ID) and/or tissue (Uberon ID); AND include ‘has_regulation_target’ mRNA (ENSEMBL transcript ID)
6b evidence in the paper of specific negative or positive regulation of mRNA; if negative/positive regulation of the mRNA is demonstrated but this is a ‘fishing’ experiment and there is no information from the author that the targets are expected to be regulated. GO:0010468 regulation of gene expression, GO:0010629 negative regulation of gene expression, GO:0010628 positive regulation of gene expression IDA or IMP 'occurs_in' cell (CL ID) and/or tissue (Uberon ID); NO ‘has_regulation_target’
7 evidence in the paper of specific negative regulation of mRNA; plus specific mRNA binding demonstrated (this could be in a different paper) new GO miRNA MF term (child of 'GO:0035195 gene silencing by miRNA') IDA or IMP 'occurs_in' cell (CL ID) and/or tissue (Uberon ID); ‘has_direct_input’ mRNA (ENSEMBL transcript ID)
Evidence code usage for annotating miRNAs

Pre-miR – adding a miR to an experiment – transfection, usually use IDA, even though this will be over-expression. If this is addition of a pre-miR that is normally expressed in that cell then the cell type can be added to C16.

Anti-miRs reverse sequence, stops miR working, use IMP and C16 cell type, if primary cells.

Question 2

Treatment with TGF-β1 decreased miR-29b expression in hAFBs

Agreed annotation: include cell specific information Human TGF-β1 GO:2000628 regulation of miRNA metabolic process IDA C16: has_regulation_target human miR-29b, occurs_in CL:0002547 fibroblast of the aortic adventitia

Action Item: comment from Questionnaire GO "expression" is not related to "metabolic processes". Address by SourceForge?

Question 3

Agreed there should there be new GO terms specific for the function of miRNAs and proteins, with part_of relationship to parent ‘gene silencing by miRNA’. To distinguish role of miRNAs and proteins in this process.

Action Item: submit request to SourceForge

Question 4 & 9

Summary: for function annotations, binding should be required, but for process annotations binding isn’t necessary. miRNA should be annotated with the new GO miRNA MF term (child of 'GO:0035195 gene silencing by miRNA') only if there is evidence in the paper of specific mRNA regulation along with mRNA binding (this could be in 2 different papers) and often will be able to include C16 information about the mRNA with qualifier ‘has_direct_input’.

Question 4 & 9

miRNA should be annotated with 'GO:0035195 gene silencing by miRNA' if this is the authors intent (ie they suggest that this is an expected target for the miRNA) and negative regulation of the mRNA is demonstrated and often will be able to include C16 information about the mRNA with qualifier ‘has_regulation_target’. Recognise that there will be occasions when these annotations are not correct, as the miR may regulate translation of gene which then regulates translation of the target mRNA. However, scientists need this information for analysis and drug design.

Question 4 & 9

miRNA should be annotated with either (negative/positive …‘GO:0010468 regulation of gene expression’ or ‘GO:0040029 regulation of gene expression, epigenetic' [attendees to confirm] if negative/positive regulation of the mRNA is demonstrated but this is a ‘fishing’ experiment and there is no information from the author that the targets are expected to be regulated. Will be able to include C16 information about the mRNA with qualifier ‘has_regulation_target’. Scientists need this information for analysis and drug design.

Action Item: confirm agreement that with IMP (anti-miR), there is no requirement to show there is binding. For a pre-miR experiment (overexpression, IDA), evidence of target being bound is required.

Question 5 & 6

If cells the authors are using are biologically relevant, capture cell in annotation extension – if just using cell type as an assay system, don’t capture it. We’re trying to represent the biology not the experiment. Try to capture C16 information about relevant cells/tissues and mRNA targets whenever there is experimental support.

Action item: Ruth to learn what relationship to use in C16 to capture that a MF or BP occurs following/in response to GO:0071560 cellular response to transforming growth factor beta stimulus. ‘happens_during’ just means it happens at the same time, not during the process.

Question 7

Downstream annotation. Users would find it useful to see this (e.g. drug targets); a key question to consider is whether scientists would expect to see the miRNA if they did query on the term. Consider author intent, may be a combination of evidence in the paper to support the annotation.

Action item: All to revisit the agreed conventions for annotation of downstream processes.

Question 8

All agreed that if the anti-miR sequence aligns 100% with complementary sequence of more than 1 miR, consider whether these miRs are all expressed in cell and the intent of the author. It maybe appropriate to annotate more than 1 miR to the GO term, using the IGI evidence code and including the other miR(s) in the WITH field.

Application of IEP vs. IDA evidence codes for annotation of response to GO term

Identified that there is a disagreement about what is meant by the GO ‘response to’ term. Example :GO:0034599 cellular response to oxidative stress, definition: Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.

The definition implies that the genes annotated should be involved in the process of changing the state/activity of the cell. It does not imply that the genes annotated will be 'genes whose expression is regulated following the changing the state/activity of the cell'.

Action item: review the ontology and definitions in this domain. Does experimental data which measures expression levels as a result of treatment information that can be captured in this domain? And if so with which evidence code: IDA or IMP? Should GO capture this information?

Items to follow up

Action Item: comment from Questionnaire GO "expression" is not related to "metabolic processes". Address by SourceForge?

Action Item: submit request to SourceForge to request new GO terms specific for the function of miRNAs and proteins, with part_of relationship to parent ‘gene silencing by miRNA’

Action Item: confirm agreement that with IMP (anti-miR), there is no requirement to show there is binding. For a pre-miR experiment (overexpression, IDA), evidence of target being bound is required.

Action item: GO editors to agree/create a relationship to use in C16 to capture that a MF or BP occurs following/in response to GO:0071560 cellular response to transforming growth factor beta stimulus. ‘happens_during’ just means it happens at the same time, not during the process.

Action item: All to revisit the agreed conventions for annotation of downstream processes.

Action item: review the 'response to' ontology and definitions in this domain. Does experimental data which measures expression levels as a result of treatment information that can be captured in this domain? And if so with which evidence code: IDA or IMP? Should GO capture this information?