PathExpand

Cellular processes and pathways, whose deregulation may contribute to the development of cancers, are often represented as cascades of proteins transmitting a signal from the cell surface to the nucleus. However, recent functional genomic experiments have challenged the traditional view of pathways as independent functional entities. Combining information from pathway databases and interaction networks is therefore a promising strategy to obtain more robust pathway and process representations.

PathExpand is a methodology for extending pre-defined protein sets representing cellular pathways and processes by mapping them onto a protein-protein interaction network, and expanding them to include densely interconnected interaction partners. The added proteins display distinctive network topological features and molecular function annotations, and can be proposed as putative new pathway components, and/or as regulators of the communication between different cellular processes.

Publications

• 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}
  }