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

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 fo

SUBMITTER: Sales G 

PROVIDER: S-EPMC3296647 | biostudies-literature | 2012 Jan

REPOSITORIES: biostudies-literature