EAT-UpTF：一组植物基因上游转录因子的富集分析工具。

EAT-UpTF: Enrichment Analysis Tool for Upstream Transcription Factors of a Group of Plant Genes.

作者信息

Shim Sangrea, Seo Pil Joon

机构信息

Department of Chemistry, Seoul National University, Seoul, South Korea.

Plant Genomics and Breeding Institute, Seoul National University, Seoul, South Korea.

出版信息

Front Genet. 2020 Sep 11;11:566569. doi: 10.3389/fgene.2020.566569. eCollection 2020.

DOI:10.3389/fgene.2020.566569

PMID:33024441

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC7516213/

Abstract

EAT-UpTF (Enrichment Analysis Tool for Upstream Transcription Factors of a group of plant genes) is an open-source Python script that analyzes the enrichment of upstream transcription factors (TFs) in a group of genes-of-interest (GOIs). EAT-UpTF utilizes genome-wide lists of TF-target genes generated by DNA affinity purification followed by sequencing (DAP-seq) or chromatin immunoprecipitation followed by sequencing (ChIP-seq). Unlike previous methods based on the two-step prediction of -motifs and DNA-element-binding TFs, our EAT-UpTF analysis enabled a one-step identification of enriched upstream TFs in a set of GOIs using lists of empirically determined TF-target genes. The tool is designed particularly for plant researches, due to the lack of analytic tools for upstream TF enrichment, and available at https://github.com/sangreashim/EAT-UpTF and http://chromatindynamics.snu.ac.kr:8080/EatupTF.

摘要

EAT-UpTF（一组植物基因上游转录因子富集分析工具）是一个开源的Python脚本，用于分析一组感兴趣基因（GOIs）中上游转录因子（TFs）的富集情况。EAT-UpTF利用通过DNA亲和纯化测序（DAP-seq）或染色质免疫沉淀测序（ChIP-seq）生成的全基因组TF靶基因列表。与以前基于两步预测基序和DNA元件结合TF的方法不同，我们的EAT-UpTF分析能够使用经验确定的TF靶基因列表一步识别一组GOIs中富集的上游TF。由于缺乏上游TF富集的分析工具，该工具专门为植物研究设计，可在https://github.com/sangreashim/EAT-UpTF和http://chromatindynamics.snu.ac.kr:8080/EatupTF获取。