Molecular_Interaction_Maps/DnaSite

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Summary

A user wants to describe a DNA site that is involved in a pathway

Step-by-Step User Action

1. User specifies that there is a DNA site
2. User labels the DNA site

Visual Aides

The notation for a DNA site is the following:

An example using this notation follows:

Requirements for Cytoscape

TBD

Importance

TBD

Other Examples

Comments

Shared ../MimEditorUseCaseComments

BioPax representation TBD

GaryBader - 2006-12-26 12:12:38

This is related to the general problem of representing sequence features in the context of a network. BioPAX Level 2 has basic support for describing sequence features (taken from PSI-MI), however Level 3 will add support for stating which sequence features are bound to others (related to describing topology of a complex).

GaryBader - 2006-12-26 12:13:16

Also, this is related to the sub-gene use case by the GenMAPP group at http://cytoscape.org/cgi-bin/moin.cgi/groupAPI/UseCase_3A

AllanKuchinsky - 2007-01-19 03:37:08

What is the formal relationship between A and A'?

MiritAladjem - 2007-02-01 08:58:10

In answer to Alan's comment: A' is a variant of A that has the binding site but not the acting site. There are real examples of such molecules (e.g. splicing variants). In the depicted case, A or A' can both bind DNA but they compete on the same site so just one of those two molecules can bind to the site at a specific time.