| NetAtlas: a Cytoscape plugin to examine signaling networks based on tissue gene expression. | |
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MedLine Citation:
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PMID: 18430989 Owner: NLM Status: MEDLINE |
Abstract/OtherAbstract:
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Graphical methods are useful for visualizing signaling networks derived from the synthesis of large bodies of literature information or large-scale experimental measurements. Software tools to filter and organize these networks allow the exploration of their inherent biological and structural properties. We have developed NetAtlas, an open-source, Java-based Cytoscape plugin for examining signaling networks in the context of tissue gene expression patterns. The tissue gene expression data available through NetAtlas consists of 79 human tissues, 61 mouse tissues, and 44 combined tissues from 3 rat strains. Users may also import their own tissue gene expression data. The NetAtlas plugin allows the creation of tissue-defined signaling networks by identifying which components are expressed in particular tissues, which components show tissue-specific expression, and which components within the network are coordinately expressed across tissues. The NetAtlas plugin is available at http://sourceforge.net/projects/netatlas/. |
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Authors:
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Longlong Yang; John R Walker; John B Hogenesch; Russell S Thomas |
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Publication Detail:
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Type: Comparative Study; Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't |
Journal Detail:
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Title: In silico biology Volume: 8 ISSN: 1386-6338 ISO Abbreviation: In Silico Biol. (Gedrukt) Publication Date: 2008 |
Date Detail:
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Created Date: 2008-04-23 Completed Date: 2008-07-22 Revised Date: - |
Medline Journal Info:
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Nlm Unique ID: 9815902 Medline TA: In Silico Biol Country: Netherlands |
Other Details:
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Languages: eng Pagination: 47-52 Citation Subset: IM |
Affiliation:
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The Hamner Institutes for Health Sciences, 6 Davis Drive, Research Triangle Park, NC 27709-2137, USA. |
Export Citation:
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| MeSH Terms | |
Descriptor/Qualifier:
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Adenocarcinoma
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genetics* Algorithms* Animals Colorectal Neoplasms / genetics* Computer Simulation Gene Expression Profiling Gene Expression Regulation, Neoplastic / physiology* Humans Mice Protein Interaction Mapping / methods* Rats Signal Transduction / genetics* Software |
| Grant Support | |
ID/Acronym/Agency:
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2 P42 ES004911-17/ES/NIEHS NIH HHS |
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine
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