Use Case Name : ../DnaSite

For Feature : MIMEditor

Editors: DavidKane

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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




Other Examples


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

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.

Molecular_Interaction_Maps/DnaSite (last edited 2009-02-12 01:03:04 by localhost)

Funding for Cytoscape is provided by a federal grant from the U.S. National Institute of General Medical Sciences (NIGMS) of the Na tional Institutes of Health (NIH) under award number GM070743-01. Corporate funding is provided through a contract from Unilever PLC.

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