Java Enrichment of Pathways Extended To Topology

JEPETTO is a Cytoscape 3.x plugin which uses our servers: EnrichNet, PathExpand and TopoGSA to analyse a user-submitted human gene set. It identifies associations between genes and pathways using protein interaction network and topological analysis.

JEPETTO performs two types of analysis. It can enrich a gene set with components from the pathways and processes closely connected in the interaction network or compare topological properties of the gene set interactions to properties of known cellular pathways and processes. The plugin allows users to infer information about biological regulatory mechanisms and identify putative new co-factors that would not have been detected using the standard term-based analysis.

Documentation

The installation process and the plugin features together with several usage examples are described in the tutorial.

Download

You can download the plugin Java source code (GNU GPLv3) or the compiled JAR file.

It is also available directly from the Cytoscape app store.

Project team

• Charles Winterhalter
• Paweł Widera
• Natalio Krasnogor

Publications

If you use JEPETTO, please cite the following publications:

• DOI eprint code BibTeX
  C. Winterhalter, P. Widera, N. Krasnogor
  JEPETTO: a Cytoscape plugin for gene set enrichment and topological analysis based on interaction networks
  in Bioinformatics, 30(7):1029-1030, April 2014

  @ARTICLE{Winterhalter2013,
    title = {JEPETTO: a Cytoscape plugin for gene set enrichment and topological analysis based on interaction networks},
    author = {Winterhalter, C. and Widera, P. and Krasnogor, N.},
    year = 2014,
    doi = {10.1093/bioinformatics/btt732},
    month = apr,
    journal = {Bioinformatics},
    volume = {30},
    number = {7},
    pages = {1029--1030}
  }
  

• DOI BibTeX
  E. Glaab, A. Baudot, N. Krasnogor, R. Schneider, A. Valencia
  EnrichNet: network-based gene set enrichment analysis
  in Bioinformatics, 28(18):i451-i457, September 2012

  @ARTICLE{Glaab2012a,
    title = {EnrichNet: network-based gene set enrichment analysis},
    author = {Glaab, E. and Baudot, A. and Krasnogor, N. and Schneider, R. and Valencia, A.},
    year = 2012,
    doi = {10.1093/bioinformatics/bts389},
    month = sep,
    journal = {Bioinformatics},
    volume = {28},
    number = {18},
    pages = {i451--i457}
  }
  

• DOI BibTeX
  E. Glaab, A. Baudot, N. Krasnogor, A. Valencia
  Extending pathways and processes using molecular interaction networks to analyse cancer genome data
  in BMC Bioinformatics, 11(1):597, 2010

  @ARTICLE{Glaab2010,
    title = {Extending pathways and processes using molecular interaction networks to analyse cancer genome data},
    author = {Glaab, Enrico and Baudot, Anaïs and Krasnogor, Natalio and Valencia, Alfonso},
    year = 2010,
    doi = {10.1186/1471-2105-11-597},
    journal = {BMC Bioinformatics},
    volume = {11},
    number = {1},
    pages = {597}
  }
  

• DOI eprint BibTeX
  E. Glaab, A. Baudot, N. Krasnogor, A. Valencia
  TopoGSA: network topological gene set analysis
  in Bioinformatics, 26(9):1271-1272, May 2010

  @ARTICLE{Glaab2010a,
    title = {TopoGSA: network topological gene set analysis},
    author = {Glaab, E. and Baudot, A. and Krasnogor, N. and Valencia, A.},
    year = 2010,
    doi = {10.1093/bioinformatics/btq131},
    month = may,
    journal = {Bioinformatics},
    volume = {26},
    number = {9},
    pages = {1271--1272}
  }