Annotation Conf. Call 2017-05-09: Difference between revisions

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***PACAP1 receptor - endocytic vesicle
***PACAP1 receptor - endocytic vesicle
***Trk - Golgi
***Trk - Golgi
**Is it appropriate to annotate a membrane protein that is a ligand for a signalling pathway in another cell to a location that is in that other cell?
***ZP3 (zona pellucida glycoprotein of oocyte) to 'outer acrosomal membrane' (of sperm cell)
**What if you don't know whether a subcellular location is a site of molecular activity?
**What if you don't know whether a subcellular location is a site of molecular activity?



Revision as of 12:32, 8 May 2017

Bluejeans URL

https://bluejeans.com/993661940

Agenda

Annotation Guidelines

Review Annotation Guidelines for Cellular Component (CC) Annotations

  • Many gene products can be found in multiple places within the cells in which they are expressed
    • Soluble secreted proteins and transmembrane proteins can be found in a number of different cytoplasmic compartments (ER, Golgi, vesicles) as they traverse the secretory pathway
    • Internalized receptors can be found in endocytic vesicles
    • Transcriptional regulators can shuttle between the cytoplasm and the nucleus
    • Secreted ligands can be found in the extracellular space and the external side of a plasma membrane when they are bound to their receptor
  • The curation guidelines for CC annotation are to annotate the gene product to the cellular/extracellular location where it is believed to be active
    • For some gene products this will be very clear
    • There are some cases where receptors found at the plasma membrane are also found to be involved in signaling pathways that occur at other locations
      • PACAP1 receptor - endocytic vesicle
      • Trk - Golgi
    • Is it appropriate to annotate a membrane protein that is a ligand for a signalling pathway in another cell to a location that is in that other cell?
      • ZP3 (zona pellucida glycoprotein of oocyte) to 'outer acrosomal membrane' (of sperm cell)
    • What if you don't know whether a subcellular location is a site of molecular activity?

Use of colocalizes_with Qualifier

 Gene products that are transiently or peripherally associated with an organelle or complex may be annotated to the relevant cellular 
 component term, using the colocalizes_with qualifier. This qualifier may also be used in cases where the resolution of an assay 
 is not accurate enough to say that the gene product is a bona fide component member. Example (from Schizosaccharomyces 
 pombe): Clp1p relocalizes from the nucleolus to the spindle and site of cell division; i.e. it is associated transiently with the spindle 
 pole body and the contractile ring (evidence from GFP fusion). Clp1p is annotated to spindle pole body; GO:0005816 and contractile 
 ring; GO:0005826, using the colocalizes_with qualifier in both cases.

Annotation and Ontology Proposals

Modification-Dependent Protein Binding

  • Proposal from Pascale and Sylvain emailed
  • Would like to review and approve proposal on this call

Transcription Decision Tree

  • AI: Review annotation decision tree which is linked from the github ticket in go-annotation
  • github ticket 1463

Minutes