Cytoscape Wiki|
← Revision 1 as of 2006-11-15 21:56:22 →
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Use Case Name : EnzymaticStimulationInTrans |
For Feature : MIMEditor |
Editors: DavidKane |
Summary
A user wants specify that a species is an enzyme that stimulates a reaction by binding with another copy of the same species
Step-by-Step User Action
- User specifies a species to be the enzymatic stimulator
- User specifies a reaction involving that species to be stimulated
- User specifies that there is a enzymatic in trans stimulation relationship
- User optionally specifies the evidence for the relationship
Visual Aides
The Kohn notation for enzymatic stimulation in trans is the following:
attachment:enzymaticstimulationintrans1_061115_dwk.png
An example using this notation follows:
attachment:enzymaticstimulationintrans2_061115_dwk.png
In this example, a copy of protein A, catalyzes the phosphorylation of another copy of protein A.
Requirements for Cytoscape
Assuming that this can use the same approach that is used for Inhibition, it could be modeled as a Hyperedge containing node1: C (hyperedge attribute: enzymatic stimulation in trans), node2: A, node3: A
View: Use case for hyperedge view
Importance
TBD
Other Examples
Comments
Shared MimEditorUseCaseComments
This is a special case of an EnzymaticStimulation. It is intended to clarify that more than one copy of a particular protein is involved in the interaction.
This could be modeled in BioPAX as a Catalysis object (e.g. Catalysis object with participants = a Biochemical Reaction object and a enzyme A, Controlled = the Biochemical Reaction object (a reaction in trans as defined in "in trans reactions"cannot communicate that is specifically a covalent phosphorylation reaction, Controller=A, Control-Type = Activation, and Direction = IRREVERSIBLE-LEFT-TO-RIGHT)