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Comment: Generalized to account for other uses of the InTrans notation
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| ## page was renamed from Molecular Interaction Maps/EnzymaticStimulationInTrans | |
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| || '''Use Case Name''' : ../EnzymaticStimulationInTrans || | || '''Use Case Name''' : ../InTrans || |
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| A user wants specify that a species is an enzyme that stimulates a reaction by binding with another copy of the same species |
A user wants specify ''in trans'', i.e. that a species is involved in an enzymatic or binding activity with another copy of the same species |
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1. User specifies a species to be the enzymatic stimulator 1. User specifies a reaction involving that species to be stimulated 1. User specifies that there is a enzymatic in trans stimulation relationship |
1. User specifies an existing enzymatic stimulation or binding activity 1. User specieis that the activity is ''in trans'' |
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As an alternative to modifying an existing relationship, this use case might be viewed as creating a different relationship in the first place, e.g. 1. User specifies a species to be the enzymatic stimulator 1. User specifies a reaction to be stimulated involving the same species 1. User specifies that there is a stimulation ''in trans'' relationship 1. User optionally specifies the evidence for the relationship |
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| attachment:enzymaticstimulationintrans1_061115_dwk.png | attachment:intrans1_061121_dwk.png |
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| An example using this notation follows: | This notation can be used to modify the edges for ../NonCovalentBinding or ../EnzymaticStimulation |
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| attachment:enzymaticstimulationintrans2_061115_dwk.png |
attachment:intrans2_061121_dwk.png attachment:intrans4_061121_dwk.png An example using this notation for ../EnzymaticStimulation follows: attachment:intrans5_061121_dwk.png |
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The following example uses intrans for a ../NonCovalentBinding relationship: attachment:intrans3_061121_dwk.png In this example, a copy of protein A, binds a domain 1 to another copy of protein A at domain 2. |
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| TBD | This is a fairly common occurance in the models. |
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== Variations == An earlier version of the notation uses small circles instead of the slashes. This earlier notation does not need to be supported. attachment:enzymaticstimulationintrans1_061115_dwk.png attachment:enzymaticstimulationintrans2_061115_dwk.png |
Summary
A user wants specify in trans, i.e. that a species is involved in an enzymatic or binding activity with another copy of the same species
Step-by-Step User Action
- User specifies an existing enzymatic stimulation or binding activity
User specieis that the activity is in trans
- User optionally specifies the evidence for the relationship
As an alternative to modifying an existing relationship, this use case might be viewed as creating a different relationship in the first place, e.g.
- User specifies a species to be the enzymatic stimulator
- User specifies a reaction to be stimulated involving the same species
User specifies that there is a stimulation in trans relationship
- User optionally specifies the evidence for the relationship
Visual Aides
The Kohn notation for enzymatic stimulation in trans is the following:
attachment:intrans1_061121_dwk.png
This notation can be used to modify the edges for ../NonCovalentBinding or ../EnzymaticStimulation
attachment:intrans2_061121_dwk.png
attachment:intrans4_061121_dwk.png
An example using this notation for ../EnzymaticStimulation follows:
attachment:intrans5_061121_dwk.png
In this example, a copy of protein A, catalyzes the phosphorylation of another copy of protein A.
The following example uses intrans for a ../NonCovalentBinding relationship:
attachment:intrans3_061121_dwk.png
In this example, a copy of protein A, binds a domain 1 to another copy of protein A at domain 2.
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
This is a fairly common occurance in the models.
Variations
An earlier version of the notation uses small circles instead of the slashes. This earlier notation does not need to be supported.
attachment:enzymaticstimulationintrans1_061115_dwk.png
attachment:enzymaticstimulationintrans2_061115_dwk.png
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)