Difference between revisions of "LEGO June 1, 2015"

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(Agenda)
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==Agenda==
 
==Agenda==
 +
 +
===LEGO Curation===
 +
====GTPase Signaling Pathways====
 +
*Annotating GTPases to reflect their role in a signaling pathway
 +
**Annotate entity as GTP-bound form (via PRO ID, for example)?
 +
**We have a term, GO:0030742, GTP-dependent protein binding; what is the intended use of this term?
 +
***Definition: Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules) using energy from the hydrolysis of GTP.
 +
*What experimental evidence supports use of:
 +
**causally_upstream_of
 +
**directly_activates
 +
**has_direct_input
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**positively_regulates
 +
 +
===Annotation Issues===
 +
*MIG-2 (C. elegans RhoG) has low affinity for GTP (similar to GTP binding-defective negative control) but GTPase activity similar to other Rho GTPases, so evidence for GTP binding is weak
 +
*Paper uses an engineered GTP-bound mimic to assess binding to downstream effector, ANI-1
 +
*What's the correct annotation for the binding? 
 +
**ANI-1: GTP-Rho binding?  Rho GTPase binding?
 +
*What's the correct MF annotation for MIG-2 for this signaling pathway?

Revision as of 06:38, 29 May 2015


Agenda

LEGO Curation

GTPase Signaling Pathways

  • Annotating GTPases to reflect their role in a signaling pathway
    • Annotate entity as GTP-bound form (via PRO ID, for example)?
    • We have a term, GO:0030742, GTP-dependent protein binding; what is the intended use of this term?
      • Definition: Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules) using energy from the hydrolysis of GTP.
  • What experimental evidence supports use of:
    • causally_upstream_of
    • directly_activates
    • has_direct_input
    • positively_regulates

Annotation Issues

  • MIG-2 (C. elegans RhoG) has low affinity for GTP (similar to GTP binding-defective negative control) but GTPase activity similar to other Rho GTPases, so evidence for GTP binding is weak
  • Paper uses an engineered GTP-bound mimic to assess binding to downstream effector, ANI-1
  • What's the correct annotation for the binding?
    • ANI-1: GTP-Rho binding? Rho GTPase binding?
  • What's the correct MF annotation for MIG-2 for this signaling pathway?