Calculating biological module enrichment or depletion and visualizing data on large-scale molecular maps with ACSNMineR and RNaviCell R packages

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, such as the Atlas of Cancer Signaling Network (ACSN). All these open biological databases facilitate analyses, improving our understanding of cellular systems. We hereby describe the R package ACSNMineR for calculation of enrichment or depletion of lists of genes of interest in biological pathways. ACSNMineR integrates ACSN molecular pathways, but can use any molecular pathway encoded as a GMT file, for instance sets of genes available in the Molecular Signatures Database (MSigDB). We also present the R package 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.