Use Case Name : ../TranscriptionInhibitionShorthand

For Feature : MIMEditor

Editors: DavidKane

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A user wants to describe the possibility that one species can inhibit transcription of a protein, without showing in detail, all of the mechanisms.

Step-by-Step User Action

  1. User specifies a species as the inhibitor
  2. User specifies a transcription reaction to inhibit
  3. User specifies that there is a ../TranscriptionInhibitionShorthand relationship between the two

  4. User optionally specifies the evidence for this reaction

Visual Aides

The symbol for ../TranscriptionInhibitionShorthand follows:


An example showing A inhibiting the transcription of B follows:


There are two right angles near the head. This can be more clearly seen when there is a longer edge.


This use case differs from ../ShowInhibition in that the mechanism represented by ../TranscriptionInhibitionShorthand is inhibition of transcription, where as ../ShowInhibition can represent any mechanism of inhibition.

Requirements for Cytoscape



This has been used infrequently, and so is of a lower priority. ../ShowInhibition is usually sufficient.

Other Examples


Shared ../MimEditorUseCaseComments

BioPax representation TBD

GaryBader - 2006-12-26 12:27:17

BioPAX - part of gene regulation proposal for next level.

AllanKuchinsky - 2007-01-22 05:18:58

can be handled by a new Edge type and associated rendering?

would require modifications to vizmapper for edge rendering, or custom edge graphics?

AllanKuchinsky - 2007-05-25 10:12:53

Actually, since the bend is hear the head of the target node, couldn't we just support it with a new type of arrowhead?  Or is it best handled as an edge with anchor points and right-angle constraints?

Molecular_Interaction_Maps/TranscriptionInhibitionShorthand (last edited 2009-02-12 01:03:45 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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