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BMC Bioinformatics. 2012 Jan 31;13:20. doi: 10.1186/1471-2105-13-20.

graphite - a Bioconductor package to convert pathway topology to gene network.

Author information

1
Department of Biology, University of Padova, via U, Bassi 58/B, Padova, Italy.

Abstract

BACKGROUND:

Gene set analysis is moving towards considering pathway topology as a crucial feature. Pathway elements are complex entities such as protein complexes, gene family members and chemical compounds. The conversion of pathway topology to a gene/protein networks (where nodes are a simple element like a gene/protein) is a critical and challenging task that enables topology-based gene set analyses.Unfortunately, currently available R/Bioconductor packages provide pathway networks only from single databases. They do not propagate signals through chemical compounds and do not differentiate between complexes and gene families.

RESULTS:

Here we present graphite, a Bioconductor package addressing these issues. Pathway information from four different databases is interpreted following specific biologically-driven rules that allow the reconstruction of gene-gene networks taking into account protein complexes, gene families and sensibly removing chemical compounds from the final graphs. The resulting networks represent a uniform resource for pathway analyses. Indeed, graphite provides easy access to three recently proposed topological methods. The graphite package is available as part of the Bioconductor software suite.

CONCLUSIONS:

graphite is an innovative package able to gather and make easily available the contents of the four major pathway databases. In the field of topological analysis graphite acts as a provider of biological information by reducing the pathway complexity considering the biological meaning of the pathway elements.

PMID:
22292714
PMCID:
PMC3296647
DOI:
10.1186/1471-2105-13-20
[Indexed for MEDLINE]
Free PMC Article

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