The plugin automatically recognizes a variety of identifiers for genes, proteins or miRNAs that can be updated with the latest NCBI information.ĬluePedia comes with human and mouse interaction data. Sets of identifiers of interest can be directly uploaded in text format, pasted in a text field or interactively derived from gene networks. The pathway analysis is based on GO ( Ashburner et al., 2000), KEGG ( Kanehisa et al., 2002), Reactome ( Croft et al., 2011) and other resources ( Supplementary Material). The user can analyze his/her own experimental data and directly compare and enrich it with publicly available information from STRING ( Szklarczyk et al., 2011), IntAct ( Kerrien et al., 2012), MiMI ( Tarcea et al., 2009), miRBase ( Kozomara and Griffiths-Jones, 2011) and miRecords ( Xiao et al., 2009).
#CYTOSCAPE PATHWAY MANUAL#
The user manual is available at the CluePedia website.Ĭontact: or information: Supplementary data are available at Bioinformatics online. The CluePedia Cytoscape plugin is user-friendly and has an expressive and intuitive visualization.Īvailability: and via the Cytoscape plugin manager. Combining all these features is essential for data interpretation and the generation of new hypotheses. A pathway-like visualization can be created using the Cerebral plugin layout. Interrelations within each pathway can be investigated, and new potential associations may be revealed through gene/protein/miRNA enrichments. Genes, proteins and miRNAs can be connected based on in silico and/or experimental information and integrated into a ClueGO network of terms/pathways. CluePedia calculates linear and non-linear statistical dependencies from experimental data. Summary: The CluePedia Cytoscape plugin is a search tool for new markers potentially associated to pathways.
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