LEGO June 1, 2015: Difference between revisions
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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 | |||
**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 10:38, 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?