DEsubs: an R package for flexible identification of differentially expressed subpathways using RNA-seq experiments

• Published in: Bioinformatics (Oxford, England) Vol. 32; no. 24; pp. 3844 - 3846
• Main Authors: Vrahatis, Aristidis G, Balomenos, Panos, Tsakalidis, Athanasios K, Bezerianos, Anastasios
• Format: Journal Article
• Language: English
• Published: England 15.12.2016
• Subjects: Humans; RNA; Sequence Analysis, RNA - methods; Software; Transcriptome
• ISSN: 1367-4803; 1367-4811
• DOI: 10.1093/bioinformatics/btw544

DEsubs is a network-based systems biology R package that extracts disease-perturbed subpathways within a pathway network as recorded by RNA-seq experiments. It contains an extensive and customized framework with a broad range of operation modes at all stages of the subpathway analysis, enabling so a case-specific approach. The operation modes include pathway network construction and processing, subpathway extraction, visualization and enrichment analysis with regard to various biological and pharmacological features. Its capabilities render DEsubs a tool-guide for both the modeler and experimentalist for the identification of more robust systems-level drug targets and biomarkers for complex diseases. DEsubs is implemented as an R package following Bioconductor guidelines: http://bioconductor.org/packages/DEsubs/ CONTACT: tassos.bezerianos@nus.edu.sgSupplementary information: Supplementary data are available at Bioinformatics online.