graphite

The "graphite" R package advances gene set analysis by incorporating pathway topology as a fundamental aspect. Traditional gene set studies often overlook the intricate topologies of pathways, where elements include not only individual genes or proteins but also complexes, gene families, and chemical compounds. Simplifying this complex pathway topology into simplified gene/protein networks for analysis poses significant challenges.

Graphite addresses these challenges by offering a comprehensive solution that combines pathway information from four major databases. It employs biologically driven rules to reconstruct gene-gene networks, effectively acknowledging protein complexes and gene families while judiciously excluding chemical compounds from the resulting networks. This approach simplifies pathway complexities into more analyzable forms without losing the essential biological significance of various pathway components.

One of graphite's key contributions is its ability to serve as a uniform resource for topology-based gene set analyses, providing users easy access to three state-of-the-art topological methods.

Topic

Functional genomics

Detail

  • Operation: Pathway or network analysis

  • Software interface: Command-line user interface,Library

  • Language: R

  • License: GNU Affero General Public License v 3.0

  • Cost: Free

  • Version name: 1.48.0

  • Credit: The University of Padova.

  • Input: -

  • Output: -

  • Contact: Gabriele Sales gabriele.sales@unipd.it

  • Collection: -

  • Maturity: Stable

Publications

  • graphite - a Bioconductor package to convert pathway topology to gene network.
  • Sales G, et al. graphite - a Bioconductor package to convert pathway topology to gene network. graphite - a Bioconductor package to convert pathway topology to gene network. 2012; 13:20. doi: 10.1186/1471-2105-13-20
  • https://doi.org/10.1186/1471-2105-13-20
  • PMID: 22292714
  • PMC: PMC3296647

Download and documentation


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