RFC Name : SubgeneViewer: Cytoscape from a Service Provider Perspective

Editor(s): Alex Pico, Allan Kuchinsky

Date: October 23, 2007

Status: Open for comment

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We are building a visualization for splice variant information for genes. This is a modular implementation, comprising the viewer (client), the service, and the database. We anticipate that this work can be generalized to an API for others to be able to develop and provide services in Cytoscape. This generalization is dependent upon the re-layering of the Cytoscape architecture.


A major new feature of Cytoscape version 2.6 is the BioWebServiceConnectivity interface, which allows Cytoscape plugin developers to write clients that connect to web services. From a different perspective, we are developing a plugin that will have both client and service components, and an underlying database that will be accessed via the service. An existing example of this kind of provision of service, server, and client is cPath.

Use Cases

An example of usage is shown in the following figure, which represents how gene information can be accessed at multiple levels of abstraction for data collected from both splicing and polymorphism microarrays.


The sub-network view provides both built-in and custom coloring schemes for accessing expression, splicing, or polymorphism data from a pathway containing gene objects. In the top panel, mock data from a splicing microarray is analyzed and visualized using the built-in Dataset Manager splicing analysis method. Here, a color is assigned to the center of each gene object on a GenMAPP-CS pathway indicating the direction of transcriptional regulation (red for up, blue for down), while the rim color of the gene indicates detection of differential splicing (red for differential splicing above a given threshold or gray for no detected change). In the middle panel, selecting the Exon and Junction view and clicking on a single gene creates a new window displaying microarray data summarized at the level of exons and splice junctions (colored lines and folds) for that same gene. In the bottom panel, a similar example is shown for a theoretical polymorphism array experiment, comparing two groups. Here specific polymorphisms with differential changes between two biological groups are displayed with Ensembl gene location annotations and dbSNP coding-level annotations (synonymous or non-synonymous).

Implementation Plan

We are implementing the service interface in a phased manner. The database itself is being developed as a research project at the Gladstone Institutes. The first version of the SubgeneViewer plugin will implement the data base a local resource, e.g. a flat file. This will migrate to a remote service interface.

We are developing our interfaces with an eye towards extracting generalizable functionality into a an API that could be used by others who would like to provide services in and to Cytoscape.

Project Management

Project Timeline

An initial version of the plugin is planned for the Cytoscape 2.7 time frame.

Generalization will depend upon the timeline for re-layering.


There will be many.


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CytoService (last edited 2009-02-12 01:03:13 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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