Cytoscape Wiki|
← Revision 4 as of 2006-11-17 16:36:36
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| || '''Use Case Name''' : Homodimer || | || '''Use Case Name''' : ../ShowHomodimer || |
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| Shared MimEditorUseCaseComments | Shared ../MimEditorUseCaseComments |
Summary
A user wants to describe the possibility that a protein molecule (modified or unmodified) binds with an identical molecule of the same protein to form a dimer.
Step-by-Step User Action
- User specifies a modified or unmodified protein that can dimerize
- User specifies that a dimer is formed
- User optionally specifies the evidence for this reaction
Visual Aides
Here is an example of the Kohn notation of a homodimer follows:
attachment:homodimer1_061115_dwk.png
Requirements for Cytoscape
TBD
Importance
Homodimerization is a very common biological process.
Variations
If the homodimer is used in a subsequent reaction, then a dot is placed in the middle. The dot in this case, represents the complex A:A.
attachment:homodimer2_061115_dwk.png
In addition to homodimers of unmodified proteins, modified proteins can also be represented forming homodimers:
attachment:homodimer3_061115_dwk.png
The color in this example is convention, and is not an essential element in the notation.
Other Examples
Comments
Shared ../MimEditorUseCaseComments
A Homodimer could be represented in BioPAX as a Complex object (e.g. Complex object with Components = A,A, where A is a physicalEntity)