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PMID: 23325622 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

CluePedia Cytoscape plugin: pathway insights using integrated experimental and in silico data.

Bioinformatics (Oxford, England) ·Vol. 29 ·No. 5 ·2013-03-01 ·Pages 661-3

Bindea G, Galon J, Mlecnik B

Abstract

The CluePedia Cytoscape plugin is a search tool for new markers potentially associated to pathways. CluePedia calculates linear and non-linear statistical dependencies from experimental data. Genes, proteins and miRNAs can be connected based on in silico and/or experimental information and integrated into a ClueGO network of terms/pathways. Interrelations within each pathway can be investigated, and new potential associations may be revealed through gene/protein/miRNA enrichments. A pathway-like visualization can be created using the Cerebral plugin layout. Combining all these features is essential for data interpretation and the generation of new hypotheses. The CluePedia Cytoscape plugin is user-friendly and has an expressive and intuitive visualization. http://www.ici.upmc.fr/cluepedia/ and via the Cytoscape plugin manager. The user manual is available at the CluePedia website.

MeSH Terms
Animals Computer Simulation Gene Regulatory Networks Humans Mice MicroRNAs/metabolism Proteins/genetics,metabolism Software
Chemicals
MicroRNAs Proteins
Authors & Affiliations
3 authors, click to expand affiliations / ORCID
Bindea Gabriela
INSERM, Laboratory of Integrative Cancer Immunology, 75006 Paris, France.
Galon Jérôme
Mlecnik Bernhard
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Article Info
Journal
Bioinformatics (Oxford, England)
Abbr.
Bioinformatics
ISSN
1367-4811
DOI
10.1093/bioinformatics/btt019
Published
2013-03-01
Epub
2013-00-16
Pages
661-3
Language
English
Region
England
NLM ID
9808944
PMCID
PMC3582273
Subset
IM
External Links
PubMed source DOI: 10.1093/bioinformatics/btt019 PMC Full Text View journal details
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