期刊
BIOINFORMATICS
卷 35, 期 24, 页码 5339-5340出版社
OXFORD UNIV PRESS
DOI: 10.1093/bioinformatics/btz573
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资金
- Ministerio de Economia y Competitividad (Spanish Ministry of Economy and Competitiveness, MINECO) [SAF2014-53819-R, SAF2017-88771-R]
- Fundacion CajaMadrid (Beca deMovilidad para Profesores de las Universidades Publicas de Madrid 2011-2012)
- Autonomous Community of Madrid (Plan Empleo Juvenil CAM 2017)
The computational identification of the transcription factors (TFs) [more generally, transcription regulators, (TR)] responsible for the co-regulation of a specific set of genes is a common problem found in genomic analysis. Herein, we describe TFEA.ChIP, a tool that makes use of ChIP-seq datasets to estimate and visualize TR enrichment in gene lists representing transcriptional profiles. We validated TFEA.ChIP using a wide variety of gene sets representing signatures of genetic and chemical perturbations as input and found that the relevant TR was correctly identified in 126 of a total of 174 analyzed. Comparison with other TR enrichment tools demonstrates that TFEA.ChIP is an highly customizable package with an outstanding performance.
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