1 / 1

Cytoscape

Cytoscape.org. Cytoscape is a freely-available bioinformatics software platform for visualizing biological networks (e.g. molecular interaction networks) and analyzing networks with gene expression profiles and other state data. Core Features

moke
Télécharger la présentation

Cytoscape

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. Cytoscape.org Cytoscape is a freely-available bioinformatics software platform forvisualizing biological networks (e.g. molecular interaction networks) andanalyzing 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.

More Related