Cytoscape Expression Viewer PlugIn

1. Introduction

Updates regarding this plugin will be posted to the Cytoscape-announce mailing list. You can easily subscribe to the mailing list or browse the archives.

2. Using the Expression Viewer Plugin

• Run the Expression Viewer Plugin (requires Java Web Start)
• Load a pathway by selecting one from the pathway list, and then clicking on the "Load Pathway" button. A good pathway to select for use with our sample expression data file is the KitReceptor. Below is a sample screenshot of the pathway list:

  
  [Click to enlarge]

• Load an expression data file by selecting the expression data tab, and then clicking on the "Browse" button. This will create a dialog box from which you can select a file containing expression data (file format notes). You can find our sample data file here (right click to download and be sure to save with .pvals extension). Below is a sample screenshot of the expression data panel:

  
  [Click to enlarge]

• After loading a pathway and expression data, the experimental conditions panel will appear. This window contains the following elements:
  • A condition selector which allows you to move between experimental conditions.
  • A color gradient which indicates for a selected node where its expression value falls in the domain of all possible expression values (denoted by a black tick mark that appears above the gradient when a node is selected).
  • A configure color theme panel which allows you to change the color gradient spectrum and/or change the MIN/CENTER/MAX values of the color gradient.
  • A legend which indicates those node(s) that contain no expression data.
  Below is a sample screenshot of the experimental conditions panel:

  
  [Click to enlarge]

3. Understanding Visual Rendering Clues

Entity	Visual Shape
Proteins, small molecules, complexes and other physical entities (as defined in the BioPAX pathway format).
Conversions, biochemical reactions, modulations and other interaction entities (as defined in the BioPAX pathway format).
Interaction Type	Arrow Shape
Inhibition
Containment, e.g. a complex can contain one or more proteins.
All other interaction types, e.g. activation, left, right, etc.
Labels for Physical Entities
All physical entities will be labeled as follows:
[NAME] [-CHEMICAL_MODIFICATION_ABBR] [(CELULAR_LOCATION_ABBR)]
where [NAME] is determined by the following order of precedence: NAME, SHORT NAME, or Shortest Synonym,
and [CHEMICAL_MODIFICATION_ABBR] and [CELLULAR_LOCATION_ABBR] are one of the abbreviations described below.
Example:
MITF:	MITF
MITF Phosphorylated:	MITF-P
MITF Phosphorylated, in the cytoplasm:	MITF-P (CP)
Abbreviations for Chemical Modifications
acetylation site	A
glycosylation site	G
phosphorylation site site	P
proteolytic cleavage site	PCS
sumoylation site	S
ubiquitination site	U
[All others]	No Abbreviation will be provided.
Abbreviations for Cellular Locations
cellular component unknown	No Abbreviation will be provided.
centrosome	CE
cytoplasm	CY
endoplasmic reticulum	ER
endosome	EN
extracellular	EM
golgi apparatus	GA
mitochondrion	MI
nucleus	NU
plasma membrane	PM
ribosome	RI
[All others]	No Abbreviation will be provided.

4. Bugs / Feature Requests

5. Contacts

Sander Group, Computational Biology Center
Memorial Sloan-Kettering Cancer Center, New York City

For any questions concerning this plugin, please contact:

This software is made available under the LGPL (Lesser General Public License).

6. Release Notes / Current Limitations

Version: 0.1

• Date: March 15, 2006
• Features:
  • Enables Cytoscape users to visualize expression data in the context of Biological Pathways.
  • Works with Cytoscape 2.2.
  • Supports all Human Affymetrix Chipsets.

Version: 0.2

• Date: June 8, 2006
• Features:
  • Includes Simplified Visual Language to describe Biological Pathways in BioPAX format.
  • Works with Cytoscape 2.3.

• It is possible (in fact, probable), that there will be multiple expression data values per network node. Which value gets used? The Expression Viewer will map over the value with the largest absolute value.
• The Expression Viewer makes no distinction between expression data in real or log values.
• Only one set of expression data can be loaded at a time. When loaded, the data will be mapped to all Pathways.