CluePedia Cytoscape plugin: pathway insights using integrated experimental and in silico data
By Gabriela Bindea, Jérôme Galon, Bernhard Mlecnik. Bioinform., 2013
1,017 citations recorded by the source corpus.
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.fr Supplementary information: Supplementary data are available at Bioinformatics online.
Subfields: Molecular Biology, Spectroscopy
View Paper: https://www.semanticscholar.org/paper/b81e2b16b11b117cafe619e3568bd50cb1b20a13
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Citations in the corpus
- Transcriptional Landscape of Human Tissue Lymphocytes Unveils Uniqueness of Tumor-Infiltrating T Regulatory Cells (2016, background): “…sophisticated bioinformatics approaches that exploit lymphocyte gene-expression data to understand the immunemodulatory networks at tumor sites, to predict clinical responses to immune-therapies, and to define therapeutic targets (Bindea et al., 2013a; Bindea et al., 2013b; Gentles et al., 2015).”