Cytoscape Wiki|
← Revision 4 as of 2006-11-17 15:49:26
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| || '''Use Case Name''' : EnzymaticStimulationInTrans || | || '''Use Case Name''' : ../EnzymaticStimulationInTrans || |
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| Assuming that this can use the same approach that is used for Self:Inhibition, it could be modeled as a Hyperedge containing node1: C (hyperedge attribute: enzymatic stimulation in trans), node2: A, node3: A | Assuming that this can use the same approach that is used for ../ShowInhibition, it could be modeled as a Hyperedge containing node1: C (hyperedge attribute: enzymatic stimulation in trans), node2: A, node3: A |
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| Shared MimEditorUseCaseComments | Shared ../MimEditorUseCaseComments |
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| 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 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. |
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 ../ShowInhibition, 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)