LEGO June 1, 2015: Difference between revisions
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*[http://www.ncbi.nlm.nih.gov/pubmed/25843030 Neuron Migration in C. elegans] | *[http://www.ncbi.nlm.nih.gov/pubmed/25843030 Neuron Migration in C. elegans] | ||
*[http://www.ncbi.nlm.nih.gov/pubmed/15814614 GTPase activities] | *[http://www.ncbi.nlm.nih.gov/pubmed/15814614 GTPase activities] | ||
*[http://go-genkisugi.rhcloud.com/seed/model/gomodel:555510740000003?barista_token=e5qro9y5275jhgicaqx3 Q cell migration model] | |||
*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 | *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 | *Paper uses an engineered GTP-bound mimic to assess binding to downstream effector, ANI-1 |
Revision as of 11:08, 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.
- Wrt linking annotons, clarify what experimental evidence supports use of:
- causally_upstream_of
- directly_activates
- positively_regulates
Annotation Issues
- Neuron Migration in C. elegans
- GTPase activities
- Q cell migration model
- 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?