Cytoscape.org

Cytoscape visualizing

is a freely-available bioinformatics software platform for biological networks (e.g. molecular interaction networks) and

analyzing

networks with gene expression profiles and other state data.

Core Features

• Customize network data display using visual styles • Powerful graph layout tools • Easily organize multiple networks • Easily navigate large networks • Filter the network • Plugin API

Input/Output

• Protein protein interactions from

BIND, TRANSFAC

databases • Gene functional annotations from Gene Ontology (

GO

) and

KEGG

databases • Biological models from Systems Biology Markup Language (

SBML

) •

cPath:

Cancer Pathway database • Proteomics Standards Initiative Molecular Interaction (PSI-MI) or Biopathway Exchange Language (BioPAX) formats • Oracle Spatial Network data model Additional features are available as

plugins

.

• •

jActiveModules:

identify significant “active” subnetworks

Expression Correlation Network

: cluster expression data •

Agilent Literature Search:

build networks by extracting interactions from scientific literature.

•

MCODE

: finds clusters of highly interconnected regions in networks •

cPath

: query, retrieve and visualize interactions from the MSKCC Cancer Pathway database •

BiNGO:

determine which Gene Ontology (GO) categories are statistically over-represented in a set of genes •

Motif Finder:

runs a Gibbs sampling motif detector on sequences for nodes in a Cytoscape network. •

CytoTalk

: Interact with Cytoscape from Perl, Python, R, shell scripts or C or C++ programs.