Cytoscape is a free software package for visualizing, modeling and analyzing molecular and genetic interaction networks. This protocol explains how to use Cytoscape to analyze the results of mRNA expression profiling, and other functional genomics and proteomics experiments, in the context of an interaction network obtained for genes of interest. Five major steps are described: (i) obtaining a gene or protein network, (ii) displaying the network using layout algorithms, (iii) integrating with gene expression and other functional attributes, (iv) identifying putative complexes and functional modules and (v) identifying enriched Gene Ontology annotations in the network. These steps provide a broad sample of the types of analyses performed by Cytoscape.

A multiple view system uses two or more distinct views to support the investigation of a single conceptual entity. Many such systems exist, ranging from computer-aided design (CAD) systems for chip design that display both the logical structure and the actual geometry of the integrated circuit to overview-plus-detail systems that show both an overview for context and a zoomed-in-view for detail. Designers of these systems must make a variety of design decisions, ranging from determining layout to constructing sophisticated coordination mechanisms. Surprisingly, little work has been done to characterize these systems or to express guidelines for their design. Based on a workshop discussion of multiple views, and based on our own design and implementation experience with these systems, we present eight guidelines for the design of multiple view systems.

Summary: GLay provides Cytoscape users an assorted collection of versatile community structure algorithms and graph layout functions for network clustering and structured visualization. High performance is achieved by dynamically linking highly optimized C functions to the Cytoscape JAVA program, which makes GLay especially suitable for decomposition, display and exploratory analysis of large biological networks.Availability: http://brainarray.mbni.med.umich.edu/glay/Contact: sugang@umich.edu