Shim Sangrea, Seo Pil Joon
Department of Chemistry, Seoul National University, Seoul, South Korea.
Plant Genomics and Breeding Institute, Seoul National University, Seoul, South Korea.
Front Genet. 2020 Sep 11;11:566569. doi: 10.3389/fgene.2020.566569. eCollection 2020.
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.
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。
