TFEA.ChIP：一个转录因子结合位点富集分析工具包，利用 ChIP-seq 数据集。

TFEA.ChIP: a tool kit for transcription factor binding site enrichment analysis capitalizing on ChIP-seq datasets.

机构信息

Departamento de Bioquímica, Universidad Autónoma de Madrid (UAM) and Instituto de Investigaciones Biomédicas 'Alberto Sols' (CSIC-UAM), Madrid, Spain.

Department of Medical Genetics, University of British Columbia Vancouver, Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Vancouver, BC V5Z 4H4, Canada.

出版信息

Bioinformatics. 2019 Dec 15;35(24):5339-5340. doi: 10.1093/bioinformatics/btz573.

DOI:10.1093/bioinformatics/btz573

PMID:31347689

Abstract

SUMMARY

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.

AVAILABILITY AND IMPLEMENTATION

TFEA.ChIP is implemented as an R package available at Bioconductor https://www.bioconductor.org/packages/devel/bioc/html/TFEA.ChIP.html and github https://github.com/LauraPS1/TFEA.ChIP_downloads. A web-based GUI to the package is also available at https://www.iib.uam.es/TFEA.ChIP/.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

摘要

在基因组分析中，鉴定负责特定基因集协同调控的转录因子（TFs）[更一般地说，转录调节剂（TR）]是一个常见的问题。本文中，我们描述了 TFEA.ChIP，这是一种利用 ChIP-seq 数据集来估计和可视化代表转录谱的基因列表中 TR 富集的工具。我们使用多种代表遗传和化学扰动特征的基因集作为输入来验证 TFEA.ChIP，发现总共分析的 174 个中有 126 个正确识别了相关的 TR。与其他 TR 富集工具的比较表明，TFEA.ChIP 是一个高度可定制的包，具有出色的性能。