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

Bioinformatics. 2013 Mar 1;29(5):661-3. doi: 10.1093/bioinformatics/btt019. Epub 2013 Jan 16.


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: and via the Cytoscape plugin manager. The user manual is available at the CluePedia website.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Computer Simulation
  • Gene Regulatory Networks*
  • Humans
  • Mice
  • MicroRNAs / metabolism
  • Proteins / genetics
  • Proteins / metabolism
  • Software*


  • MicroRNAs
  • Proteins