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ToppCluster
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ToppCluster

ToppCluster is a web-based tool for the enrichment and network analysis of mammalian RNA-seq data. ToppCluster allows visualization using R, TreeView, GenePattern, Cytoscape, and Gephi.



ToppCluster

ToppCluster is a web-based tool for the enrichment and network analysis of mammalian RNA-seq data. ToppCluster allows visualization using R, TreeView, GenePattern, Cytoscape, and Gephi.

Topic

Molecular interactions, pathways and networks; Functional, regulatory and non-coding RNA; Transcription factors and regulatory sites; Genotype and phenotype; Gene structure

Details

  • Operation: Gene regulatory network analysis; Gene-set enrichment analysis; Weighted correlation network analysis
  • Software interface: Web user interface
  • Language: R
  • Operating system: Linux; Mac OS X; Microsoft Windows
  • License: Not stated
    • Cost: Free
  • Version name: -
  • Credit: National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Diseases (NIH/NIDDK). Murine Atlas of a Genitourinary Development Molecular Anatomy Project), Cincinnati Digestive Health Center, Cincinnati Center for Clinical and Translational Sciences.
  • Contact: Anil.Jegga _at_ cchmc.org | Dr. Bruce J. Aronow, Professor Bruce.Aronow _at_ cchmc.org
  • Collection: -

Publications

Kaimal V, Bardes EE, Tabar SC, Jegga AG, Aronow BJ "ToppCluster: a multiple gene list feature analyzer for comparative enrichment clustering and network-based dissection of biological systems." Nucleic Acids Res. 2010 Jul;38(Web Server issue):W96-102. 10.1093/nar/gkq418. Epub 2010 May 19. https://doi.org/10.1093/nar/gkq418
PMID: 20484371
PMCID: PMC2896202


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