ArticleBioinformatics (Oxford, England)2019
gep2pep: a Bioconductor package for the creation and analysis of pathway-based expression profiles.
Article in Bioinformatics (Oxford, England), 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers, 1 of them a synthesis that pooled it.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
6 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Identification of therapeutic targets in osteoarthritis by combining heterogeneous transcriptional datasets, drug-induced expression profiles, and known drug-target interactions.Journal of translational medicine · 2024Pooled it
- Differentially expressed transcripts associated with depressive symptoms during pregnancy and postpartum.Molecular psychiatry · 2025Article
- Refate identifies chemical compounds to target trans-regulatory networks for cellular conversion.bioRxiv : the preprint server for biology · 2025Article
- Computational Drug Repurposing for Alzheimer's Disease Using Risk Genes From GWAS and Single-Cell RNA Sequencing Studies.Frontiers in pharmacology · 2021Article
- Identification of Novel Potential Genes Involved in Cancer by Integrated Comparative Analyses.International journal of molecular sciences · 2020Article
- Computational drug repurposing for inflammatory bowel disease using genetic information.Computational and structural biotechnology journal · 2019Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
summaryPathway-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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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.