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.

Sales, G.; Calura, E.; Cavalieri, D.; Romualdi, C. (2012). Graphite - a Bioconductor package to convert pathway topology to gene network. BMC BIOINFORMATICS, 13 (20). doi: 10.1186/1471-2105-13-20 handle: http://hdl.handle.net/10449/20920

Graphite - a Bioconductor package to convert pathway topology to gene network

Cavalieri, Duccio;
2012-01-01

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.
2012
Sales, G.; Calura, E.; Cavalieri, D.; Romualdi, C. (2012). Graphite - a Bioconductor package to convert pathway topology to gene network. BMC BIOINFORMATICS, 13 (20). doi: 10.1186/1471-2105-13-20 handle: http://hdl.handle.net/10449/20920
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Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/10449/20920
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