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- Title
CluePedia Cytoscape plugin: pathway insights using integrated experimental and in silico data.
- Authors
Bindea, Gabriela; Galon, Jérôme; Mlecnik, Bernhard
- Abstract
Summary: 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.Availability: http://www.ici.upmc.fr/cluepedia/ and via the Cytoscape plugin manager. The user manual is available at the CluePedia website.Contact: bernhard.mlecnik@crc.jussieu.fr or jerome.galon@crc.jussieu.frSupplementary information: Supplementary data are available at Bioinformatics online.
- Subjects
DATA analysis; SEARCH engines; PROTEIN genetics; COMPUTATIONAL biology; GENETIC markers; QUANTITATIVE research
- Publication
Bioinformatics, 2013, Vol 29, Issue 5, p661
- ISSN
1367-4803
- Publication type
Article
- DOI
10.1093/bioinformatics/btt019