Statistics, Department of

The R Journal
Date of this Version
12-2016
Document Type
Article
Citation
The R Journal (December 2016) 8(2); Editor: Michael Lawrence
Abstract
Biological pathways or modules represent sets of interactions or functional relationships occurring at the molecular level in living cells. A large body of knowledge on pathways is organized in public databases such as the KEGG, Reactome, or in more specialized repositories, the Atlas of Cancer Signaling Network (ACSN) being an example. All these open biological databases facilitate analyses, improving our understanding of cellular systems. We hereby describe ACSNMineR for calculation of enrichment or depletion of lists of genes of interest in biological pathways. ACSNMineR integrates ACSNmolecular pathways gene sets, but can use any gene set encoded as a GMT file, for instance sets of genes available in the Molecular Signatures Database (MSigDB). We also present RNaviCell, that can be used in conjunction with ACSNMineR to visualize different data types on web-based, interactive ACSN maps. We illustrate the functionalities of the two packages with biological data taken from large-scale cancer datasets.
Included in
Numerical Analysis and Scientific Computing Commons, Programming Languages and Compilers Commons
Comments
Copyright 2016, The R Foundation. Open access material. License: CC BY 3.0 Unported