Annotation Conf. Call 2018-06-12: Difference between revisions

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***Downstream targets, e.g. Myc and cyclin D, should not be annotated to canonical Wnt signaling  
***Downstream targets, e.g. Myc and cyclin D, should not be annotated to canonical Wnt signaling  
****Information about downstream targets could be captured, for example, as transcriptional targets in AEs, or better yet, in GO-CAM models that can more expressively show how they fit into a specific canonical Wnt signaling pathway
****Information about downstream targets could be captured, for example, as transcriptional targets in AEs, or better yet, in GO-CAM models that can more expressively show how they fit into a specific canonical Wnt signaling pathway
***Upstream components
****Gene products involved in secretion could be annotated to 'Wnt protein secretion' for now; GO-CAM models will also help to capture this information better


=== Extracellular Matrix ===
=== Extracellular Matrix ===

Revision as of 13:54, 11 June 2018

Meeting URL

GO Annotation Meetings

  • Still will be Tuesdays at 8am PDT
  • Proposed meeting schedule:
    • 1st Tuesday: Alliance Gene Function
    • 2nd Tuesday: GO Consortium
    • 3rd Tuesday: Alliance Gene Function/GO-CAM Working Group
    • 4th Tuesday: GO-CAM Working Group
    • 5th Tuesday: ad hoc, as needed

Annotation Reviews

Signaling Projects

GPCR

MAPK

JAK-STAT

Canonical Wnt Signaling

  • Review annotations wrt GO:0090090 'negative regulation of canonical Wnt signaling pathway'
    • Outstanding reviews: BHF-UCL, MGI, PARL, UniProt, Zfin
  • Review annotations wrt GO:0060070 'canonical Wnt signaling pathway'
    • Outstanding reviews: ARUK-UCL, BHF-UCL, DFLAT, MGI, ParkinsonsUK-UCL, UniProt, WB, Zfin
    • Annotation questions:
      • Wnt ligands can be part of canonical, non-canonical pathways and, as well, as part of one type of Wnt signaling pathway, can regulate another type of Wnt signaling pathway
        • Therefore, it's difficult to say definitively which Wnts are part of which types of Wnt signaling pathways; the experiments and context should be the guiding information
      • Downstream targets, e.g. Myc and cyclin D, should not be annotated to canonical Wnt signaling
        • Information about downstream targets could be captured, for example, as transcriptional targets in AEs, or better yet, in GO-CAM models that can more expressively show how they fit into a specific canonical Wnt signaling pathway
      • Upstream components
        • Gene products involved in secretion could be annotated to 'Wnt protein secretion' for now; GO-CAM models will also help to capture this information better

Extracellular Matrix

Transcription

Annotation File Pipelines

Minutes

On call: