AUTHOR=Shim Sangrea , Seo Pil Joon 

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

JOURNAL=Frontiers in Genetics

VOLUME=11

YEAR=2020

URL=https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2020.566569

DOI=10.3389/fgene.2020.566569

ISSN=1664-8021

ABSTRACT=<p>EAT-UpTF (<underline>E</underline>nrichment <underline>A</underline>nalysis <underline>T</underline>ool for <underline>Up</underline>stream <underline>T</underline>ranscription <underline>F</underline>actors 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 <italic>cis</italic>-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 <ext-link ext-link-type="uri" xlink:href="https://github.com/sangreashim/EAT-UpTF" xmlns:xlink="http://www.w3.org/1999/xlink">https://github.com/sangreashim/EAT-UpTF</ext-link> and <ext-link ext-link-type="uri" xlink:href="http://chromatindynamics.snu.ac.kr:8080/EatupTF" xmlns:xlink="http://www.w3.org/1999/xlink">http://chromatindynamics.snu.ac.kr:8080/EatupTF</ext-link>.</p>