10 AUG 2010 RefGen Phone Conference (Archived)
Kara Dolinski, Mike Livstone
WNTs have cytokine activity [Ruth/Alex]
- see PMID:18986540
- Wnts identified as affecting the formation of synapses is controlling an effector function of cells.
- Note due to lack of information provided in this paper only Wnt5a (R&D Systems only sells mouse Wnt5a) and Wnt7a (R&D Systems only sells human Wnt7a) can be annotated.
Update on annotations from all groups
- Many groups seem to be up to date. Are there any comments/problems?
- We have asked the ontology development to process ref genome SF items with higher priority. Please use the SF priority settings and set to a higher priority when you submit a ref genome request.
Tree annotation [Mike]
I began PAINTing PTHR12027, the Wnt family, Monday August 2, two weeks after the literature curation, to allow time for the annotations to percolate into PAINT. Since the literature curation went for 2 weeks, I am allowing myself a little extra time beyond the standard 1 week to PAINT this family. Here is a preliminary list of questions that have arisen so far.
Questions for MOD curators
- Worm: GO:0004871 "signal transducer activity" has the comment "Ligands do NOT have the molecular function 'signal transducer activity'." Can you please clarify the 4871 IGI on wnt-2?
- All: There are multiple annotations to "plasma membrane." Do you agree that this is valid for a ligand?
- All: There is 1 annotation to GO:0045121 "membrane raft" (Drosophila wingless, PMID 15166250). I've propagated it to the entire Wnt1/Wnt3 clade, but haven't found any other literature to support such an annotation for any Wnt. Comments would be appreciated.
- Danio: Should either of the GO:0030178 "negative regulation of Wnt receptor signaling pathway" IGI's be to the child term GO:0090090 "negative regulation of canonical Wnt receptor signaling pathway"?
- All: Even though there is a major reconfiguration of the transcription part of the ontology underway, please consider using more specific terms whenever possible. Examples:
GO:0010628 "positive regulation of gene expression" OR GO:0045449 "regulation of transcription" GO:0043193 "positive regulation of gene-specific transcription" GO:0010552 "positive regulation of gene-specific transcription from RNA polymerase II promoter"
or the corresponding negative regulation terms if appropriate.
- Mouse: Do you recommend propagating the Wnt10a GO:0014033 "neural crest cell differentiation" IDA from PMID 17286598 (MGI 3712614) to the rest of the Wnt10a's? I can't access the fulltext paper.
- Mouse: Should the Wnt7a GO:0016055 "Wnt receptor signaling pathway" IDA from PMID 19497282, "Wnt7a activates the planar cell polarity pathway to drive the symmetric expansion of satellite stem cells," actually be to GO:0060071 "Wnt receptor signaling pathway, planar cell polarity pathway"?
- Rat and Mouse: Mouse Wnt7a has an annotation to GO:0050770 "regulation of axonogenesis." Rat Wnt7b has an annotation to GO:0032536 "regulation of cell projection size" from PMID 18177422; the abstract of this paper states, "Ectopic wnt7b overexpression was sufficient to rescue neurite outgrowth in NGF-treated p53-silenced PC12 cells." Is this sufficient to generalize "regulation of axonogenesis" to both Wnt 7a and -7b? Put another way, are PC12 "neurite outgrowths" sufficiently axon-like that this is probably the same process?
- Zebrafish: wnt8a and -8b have annotations to GO:0001654 "eye development." Please specify that this is "camera-type" (GO:0043010) and consider more specific child terms such as "embryonic" (GO:0031076), "morphogenesis" (GO:0048593), or both (GO:0048596).
- Mouse: For Wnt10b GO:0043586 "tongue development," would you prefer the child term GO:0061196 "fungiform papilla development"? The reference (PMID 17284610) states "Shh expression in fungiform papillae and formation of normal mature fungiform papillae depend on signaling through Wnt and beta-catenin."
- Mouse: For Wnt6, instead of GO:0048754 "branching morphogenesis of a tube" from PMID 11948913, would you prefer GO:0001658 "branching involved in ureteric bud morphogenesis"? Instead of GO:0035148 "tube formation," would you prefer GO:0072079 "nephron tubule formation"?
Questions for ontology curators
- Is there a plan to make GO:0005110 "frizzled-2 binding" a child of GO:0005109 "frizzled binding" as described in SF # 3025937?
- Does GO:0060070 "canonical Wnt receptor signaling pathway" has_part "regulation of gene expression" or something like it?
- Should GO:0060071 "Wnt receptor signaling pathway, planar cell polarity pathway," defined as "The series of molecular signals initiated by binding of a Wnt protein to a receptor on the surface of the target cell where activated receptors signal via downstream effectors including C-Jun N-terminal kinase (JNK) to modulate cytoskeletal elements and control cell polarity," has_part GO:0007254 "JNK cascade" or something like it?
Subfamilies annotation report from Mary Dolan
I have put together a report (subfamilies.xlsx posted ftp://ftp.informatics.jax.org/pub/curatorwork/Pascale/) that summarizes the GO annotation status (as of August 1,2010) of Panther subfamilies according to the type of annotation for each refG organism. This is similar to something I had done for the old PPOD clusters.
There are separate sheets for function, process, and component. For each subfamily that contains a refG organism member, I display the type (color-coded) of annotation: experimental (green), ISS-type (yellow), other (red), or none (an organism entry for the subfamily indicates that it has a subfamily member, the slot will be empty if the organism has none). I include ICs as experimental annotations; ND annotations are not counted. I have added a few mappings from panther ids to ga file ids for completeness.
The numbers on the 'annotation_counts' sheet should be useful information for the GO grant renewal in that they give an indication of how much data that is already available in MOD ga files from years of annotation effort might be used by other annotation groups via the refG/Panther project. I think the numbers are quite impressive.
For example, of the 69,566 panther subfamilies: 32,991 have one or more model organism members (14,583 have two or more refG members). Of these 32,991 refG member subfamilies: 24,265 have some GO function annotation to one or more organisms; 15,276 have either experimental or ISS annotation; and 11,653 have experimental annotation. The numbers are similar for process and component.
I see this as complementary to the careful group by group literature curation followed by PAINT review, which, of course, provides the best comprehensive annotation. This provides a view of the maximum possible gain of shared information we could get for 'free' for other refG MODs or other genome annotation groups for their organism's Panther subfamily genes.
The report also has sheets with various counts of things -- e.g. how many genes for each organism in each subfamily. I have also done this report for panther families but I think the idea of shared information might apply more to subfamilies.
Hoping this will be useful, I look forward to your comments. Thanks. Mary
Mary E. Dolan, Ph.D.
Action items from last call
- Review annotation guidelines: http://wiki.geneontology.org/index.php/Guidelines_from_Annotation_Camp
Action items for the Sept GOC meeting
- Action: All annotation groups to review PAINT annotation sets with a view to integrating them into their association files [all groups]. Manager: Pascale
- Are all groups okay with integrating annotations in terms of the review process?
- Action: Reference Genome group needs to explore ways of improving the target list selection method to ensure a greater participation by all curation groups [Pascale and Kara].
- Now doing wnt pathway. Do we have suggestions for future projects?
- Action: Figure out a mechanism by which taxonomic restrictions derived from PAINT could be fed back into the ontology taxon restrictions file [Paul and Jane]. Manager: Jane.
- Pascale emailed Jane and Paul to check the status of that one.
PAINT GAF files
Following last month's call: Suzi will write a script to run on a regular basis (daily? weekly?) either from Berkeley or at Stanford. This script will generate 13 GAF files and place them in the go/gene-associations directory where the other gaf files are kept. These files will be named thusly:
gene_association.paint_XXX.gz (where XXX will be substituted by the name of one of the ref. genome organisms) gene_association.paint_other.gz (for the platypus, opossums, and all the other non-ref. genome organisms)
If a MOD curator decides they would like to look at a particular annotation they would still have the option of retrieving all the files needed to load that particular family into PAINT from the file directory located here: go/gene-associations/submission/paint/PTHRnnnnn (where nnnnn is the number of that family). The script will be using these as the source to build the files listed above.