Diff for "Molecular_Interaction_Maps/InTrans"

TableOfContents([2])

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

1. User specifies a species to be the enzymatic stimulator
2. User specifies a reaction involving that species to be stimulated
3. User specifies that there is a enzymatic in trans stimulation relationship
4. 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)

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