Use Case Name : Paralogs

For Feature : Groups

Editors: Kristina Hanspers


To represent two or more protein paralogs that can perform the same step in a pathway, we would like to group these. The set of proteins represent a logical OR, where either one of them alone can perform the reaction in question. To reduce complexity and enhance readability, it would be desirable to have these exhibit the properties of a group, in terms of collapsing etc, especially if there are many occurances of paralogs in one pathway.

Step-by-Step User Action

Creating a New Group of Paralogs

  1. Select two or more nodes
  2. Choose "Group Paralogs" or just “Group” (don’t know how specific this needs to be for the user) from a context menu, main menu or toolbar
  3. Automatically view collapsed view of group with default label (editable)
  4. Be able to expand group as vertically stacked set of nodes by a very simple mechanism (e.g., click on a plus/minus icon)
    1. perhaps other restricted views of the children will be allowed:
      1. horizontal stack
      2. block (e.g., 2x2, 3x4)
      3. overlapping "clump" of nodes packed into a some defined circular area
  5. Be able to destroy group
  6. Be able to expand-all or collapse-all groups in a given network

Loading a Network with Paralog Groups

  1. Same as 3-6 above

Visual Aides


In this GenMAPP pathway, stacked gene objects help indicate complex and paralog groups. For example, Dvl paralogs.

Requirements for Cytoscape


Paralogs appear on many pathways, and being able to group them is important for readability of complex pathways.

Other Examples


groupAPI/UseCase_5A (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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