gep2pep: a bioconductor package for the creation and analysis of pathway-based expression profiles

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 analysi...

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Detalles Bibliográficos
Autores principales: Napolitano, Farancesco, Carrella, Diego, Gao, Xin, di Bernardo, Diego
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2020
Materias:
Applications Note
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7703749/
https://www.ncbi.nlm.nih.gov/pubmed/31647521
http://dx.doi.org/10.1093/bioinformatics/btz803
Descripción
Sumario: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 Bioinformatics online.

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