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Updated: Jan 5, 2026
A Pathway Association Study Tool for GWAS Analyses of Metabolic Pathway Information
Published on: July 1, 2020
gep2pep: a Bioconductor package for the creation and analysis of pathway-based expression profiles
Farancesco Napolitano1,2, Diego Carrella1, Xin Gao2
1Telethon Institute of Genetics and Medicine (TIGEM), Via Campi Flegrei 34, Pozzuoli (NA), Italy.
Summary:
Pathway-based expression profiles allow for high-level interpretation of transcriptomic data and systematic comparison of dysregulated cellular programs. We have previously demonstrated the efficacy of pathway-based approaches with two different applications: the Drug Set Enrichment Analysis and the Gene2drug analysis. Here we present a software tool that allows to easily convert gene-based profiles to pathway-based profiles and analyze them within the popular R framework. We also provide pre-computed profiles derived from the original Connectivity Map and its next generation release, i.e. the LINCS database.
Availability And Implementation:
the tool is implemented as the R/Bioconductor package gep2pep and can be freely downloaded from https://bioconductor.org/packages/gep2pep.
Supplementary Information:
Supplementary data are available at http://dsea.tigem.it/lincs.
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