Table_2_EAT-UpTF: Enrichment Analysis Tool for Upstream Transcription Factors of a Group of Plant Genes.XLSX

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 cis-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（Enrichment Analysis Tool for Upstream Transcription Factors of a group of plant genes，即植物基因集上游转录因子富集分析工具）是一款开源Python脚本，可用于分析目标基因集（Genes-of-Interest，GOIs）内上游转录因子（Transcription Factors，TFs）的富集情况。该工具依托通过DNA亲和纯化测序（DNA affinity purification followed by sequencing，DAP-seq）或染色质免疫共沉淀测序（chromatin immunoprecipitation followed by sequencing，ChIP-seq）得到的全基因组转录因子靶基因列表开展分析。与以往基于顺式作用元件基序与DNA元件结合转录因子两步预测的分析方法不同，本工具可利用实验验证得到的转录因子靶基因列表，一步完成目标基因集中富集上游TFs的鉴定。鉴于当前缺乏针对植物上游转录因子富集的分析工具，该工具专为植物研究人员设计，可通过https://github.com/sangreashim/EAT-UpTF及http://chromatindynamics.snu.ac.kr:8080/EatupTF获取并使用。