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 ACSN molecular 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.
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For attribution, please cite this work as
Deveau, et al., "Calculating Biological Module Enrichment or Depletion and Visualizing Data on Large-scale Molecular Maps with ACSNMineR and RNaviCell Packages", The R Journal, 2016
BibTeX citation
@article{RJ-2016-047,
author = {Deveau, Paul and Barillot, Emmanuel and Boeva, Valentina and Zinovyev, Andrei and Bonnet, Eric},
title = {Calculating Biological Module Enrichment or Depletion and Visualizing Data on Large-scale Molecular Maps with ACSNMineR and RNaviCell Packages},
journal = {The R Journal},
year = {2016},
note = {https://doi.org/10.32614/RJ-2016-047},
doi = {10.32614/RJ-2016-047},
volume = {8},
issue = {2},
issn = {2073-4859},
pages = {293-306}
}