PTHR12027

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PTHR12027 tree annotation discussion

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

MF

  • 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?

I removed the manual IGI annotation to signal transducer activity, but also noticed that we have the same annotation in WB as an IEA via the InterPro2GO mapping. This annotation also gets applied to the other C. elegans Wnts via the same mapping.

InterPro:IPR005816 Secreted growth factor Wnt protein > GO:signal transducer activity ; GO:0004871

There are some others in the InterPro2GO mappings file that should also be checked:

InterPro:IPR005817 Wnt superfamily > GO:signal transducer activity ; GO:0004871 InterPro:IPR009139 Wnt-1 protein > GO:signal transducer activity ; GO:0004871

(and many other Wnt-number proteins share this mapping)

I'll submit this as a SourceForge item.

--Kimberly

CC

  • 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.

BP

  • 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?


This will have text from the evidence.txt file and comments from annotators


PTHR12027 (subfamily): Jan 2010 targets

This is for the lung branching morphogenesis annotation project

  • CAEEL|WB=WBGene00000858|UniProtKB=P34889
  • CHICK|ENTREZ=374243|UniProtKB=Q98SN7
  • CHICK|ENTREZ=395703|UniProtKB=Q9YGX6
  • CHICK|ENTREZ=417769|UniProtKB=A0M8U2
  • CHICK|ENTREZ=418154|UniProtKB=Q3L255
  • DANRE|ZFIN=ZDB-GENE-030717-2|UniProtKB=Q8AY89
  • DANRE|ZFIN=ZDB-GENE-060328-3|UniProtKB=A7E271
  • DANRE|ZFIN=ZDB-GENE-060824-6|UniProtKB=Q1L130
  • DANRE|ZFIN=ZDB-GENE-980526-416|UniProtKB=Q92048
  • DANRE|ZFIN=ZDB-GENE-980526-87|UniProtKB=Q92050
  • DROME|FB=FBgn0010194|UniProtKB=P28466
  • HUMAN|ENSEMBL=ENSG00000105989|UniProtKB=P09544
  • HUMAN|ENSEMBL=ENSG00000111186|UniProtKB=Q9H1J7
  • HUMAN|ENSEMBL=ENSG00000114251|UniProtKB=P41221
  • HUMAN|ENSEMBL=ENSG00000134245|UniProtKB=Q93097
  • MOUSE|MGI=MGI=1261834|UniProtKB=O70283
  • MOUSE|MGI=MGI=98954|UniProtKB=P21552
  • MOUSE|MGI=MGI=98958|UniProtKB=P22725
  • MOUSE|MGI=MGI=98959|UniProtKB=P22726
  • RAT|RGD=621346|UniProtKB=Q2IBD1
  • RAT|RGD=628850|UniProtKB=Q8CFB3
  • RAT|RGD=69250|UniProtKB=Q9QXQ7
  • RAT|RGD=69346|UniProtKB=Q9QXK5