Cytoscape

Cytoscape
Cytoscape
CytoscapeHome.png
Cytoscape home page
Stable release 2.8.2 / 18 August 2011
Operating system Any (Java-based)
License LGPL
Website Cytoscape home

Cytoscape is an open source bioinformatics software platform for visualizing molecular interaction networks and integrating with gene expression profiles and other state data. Additional features are available as plugins. Plugins are available for network and molecular profiling analyses, new layouts, additional file format support and connection with databases and searching in large networks. Plugins may be developed using the Cytoscape open Java software architecture by anyone and plugin community development is encouraged.[1][2]

Contents

History

Cytoscape was originally created at the Institute of Systems Biology in Seattle in 2002. Now, it is developed by an international consortium of open source developers. Cytoscape was initially made public in July, 2002 (v0.8); the second release (v0.9) was in November, 2002. and v1.0 was released in March 2003. Version 1.1.1 is the last stable release for the 1.0 series. Version 2.0 was initially released in 2004; Cytoscape 2.5 was released in July 2007. The last version is 2.8.2, released in August 2011.

Development

The Cytoscape core developer team continues to work on this project and in the near future, is going to release next major version, Cytoscape 3.0. It will be a more modularized, expandable and maintainable version of Cytoscape. For more information about version 3.0, see the developer's wiki page.

Usage

Yeast Protein-Protein/Protein-DNA interaction network visualized by Cytoscape. Node degree is mapped to node size

While Cytoscape is most commonly used for biological research applications, it is agnostic in terms of usage. Cytoscape can be used to visualize and analyze network graphs of any kind involving nodes and edges (e.g., social networks). A key aspect of the software architecture of Cytoscape is the use of plugins for specialized features. Plugins are developed by core developers and the greater user community.

Features

Input

  • Input and construct molecular interaction networks from raw interaction files (SIF format) containing lists of protein-protein and/or protein-DNA interaction pairs. For yeast and other model organisms, large sources of pairwise interactions are available through the BIND and TRANSFAC databases. User-defined interaction types are also supported.
  • Load and save previously-constructed interaction networks in GML format (Graph Modelling Language).
  • Load and save networks and node/edge attributes in an XML document format called XGMML (eXtensible Graph Markup and Modeling Language).
  • Input mRNA expression profiles from tab- or space-delimited text files.
  • Load and save arbitrary attributes on nodes and edges. For example, input a set of custom annotation terms for your proteins, create a set of confidence values for your protein-protein interactions.
  • Import gene functional annotations from the Gene Ontology (GO) and KEGG databases.
  • Directly import GO Terms and annotations from OBO and Gene Association files.
  • Load and save state of the Cytoscape session in a Cytoscape Session (.cys) file. Cytoscape Session file includes networks, attributes (for node/edge/network), Desktop states (selected/hidden nodes and edges, window sizes), Properties, and Visual Styles.

Visualization

  • Customize network data display using powerful visual styles.
  • View a superposition of gene expression ratios and p-values on the network. Expression data can be mapped to node color, label, border thickness, or border color, etc. according to user-configurable colors and visualization schemes.
  • Layout networks in two dimensions. A variety of layout algorithms are available, including cyclic and spring-embedded layouts.
  • Zoom in/out and pan for browsing the network.
  • Use the network manager to easily organize multiple networks. And this structure can be saved in a session file.
  • Use the bird's eye view to easily navigate large networks.
  • Easily navigate large networks (100,000+ nodes and edges) by efficient rendering engine.

Analysis

  • Plugins available for network and molecular profile analysis. For example:
    • Filter the network to select subsets of nodes and/or interactions based on the current data. For instance, users may select nodes involved in a threshold number of interactions, nodes that share a particular GO annotation, or nodes whose gene expression levels change significantly in one or more conditions according to p-values loaded with the gene expression data.
    • Find active subnetworks/pathway modules. The network is screened against gene expression data to identify connected sets of interactions, i.e. interaction subnetworks, whose genes show particularly high levels of differential expression. The interactions contained in each subnetwork provide hypotheses for the regulatory and signaling interactions in control of the observed expression changes.
    • Find clusters (highly interconnected regions) in any network loaded into Cytoscape. Depending on the type of network, clusters may mean different things. For instance, clusters in a protein-protein interaction network have been shown to be protein complexes and parts of pathways. Clusters in a protein similarity network represent protein families.

References

  1. ^ Shannon P, Markiel A, Ozier O, et al. (2003). "Cytoscape: a software environment for integrated models of biomolecular interaction networks". Genome Res. 13 (11): 2498–504. doi:10.1101/gr.1239303. PMC 403769. PMID 14597658. http://www.genome.org/cgi/content/full/13/11/2498. 
  2. ^ Bell GW, Lewitter F (2006). "Visualizing networks". Meth. Enzymol. 411: 408–21. doi:10.1016/S0076-6879(06)11022-8. PMID 16939803. 

External links

See also


Wikimedia Foundation. 2010.

Игры ⚽ Нужно решить контрольную?

Look at other dictionaries:

  • National Center for Integrative Biomedical Informatics — The National Center for Integrative Biomedical Informatics (NCIBI) is one of seven National Centers for Biomedical Computing funded by the National Institutes of Health s (NIH) Roadmap for Medical Research.[1][2]. The center is based at the… …   Wikipedia

  • Protein-protein interaction — Protein protein interactions refer to the association of protein molecules and the study of these associations from the perspective of biochemistry, signal transduction and networks. The interactions between proteins are important for many… …   Wikipedia

  • GenMAPP — Infobox Software name = GenMAPP caption = Screenshot of GenMAPP author = developer = released = latest release version = latest release date = latest preview version = latest preview date = programming language = operating system = Windows… …   Wikipedia

  • Biological network inference — Many types of biological networks exist. Few such networks are known in anything approaching their complete structure, even in the simplest bacteria. Still less is known on the parameters governing the behavior of such networks over time, how the …   Wikipedia

  • Graph Modelling Language — (GML) is a hierarchical ASCII based file format for describing graphs. Applications supporting GML * Cytoscape, an open source bioinformatics software platform for visualizing molecular interaction networks, loads and save previously constructed… …   Wikipedia

  • XGMML — (the eXtensible Graph Markup and Modeling Language) is an XML application based on GML which is used for graph description. Technically, while GML is not related to XML nor SGML, XGMML is an XML application that is so designed that there s a 1:1… …   Wikipedia

  • Biomolecular Object Network Databank — The Biomolecular Object Network Databank (BOND) is a bioinformatics databank containing information on small molecule and protein sequences, structures and interactions. The databank integrates a number of existing databses to provide a… …   Wikipedia

  • SUMO network — consists of enzymes and substrates involved in the dynamic posttranslational modification process of sumoylation (i.e. transfer of SUMO protein to substrates). Network membersThe SUMO network members (gene name and aliases) as published in the… …   Wikipedia

  • Autophagy network — consists of enzymes and substrates involved in the degradation of a cell s own components. Network membersThe Autophagy network members (gene name and aliases) as published in the last 500 newest PubMed entries (see below) are depicted… …   Wikipedia

  • DAVIX — 1.0.1 Company / developer Jan Monsch, Raffael Marty …   Wikipedia

Share the article and excerpts

Direct link
Do a right-click on the link above
and select “Copy Link”