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

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 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.

CisCross: A gene list enrichment analysis to predict upstream regulators in Arabidopsis thaliana

“…Although it is user-friendly and available online, one can not specify the promoter length or change the statistical analysis procedure there. An alternative command-line tool EAT-UpTF also utilizes the Plant Cistrome TF binding profiles ( Shim and Seo, 2020 ). Although it is not available online and requires some programming skills, one can adjust some steps in the analysis, e.g., modify the length of the 5′-regulatory regions in the analysis.…”

“…Enrichr, a comprehensive gene list enrichment analysis web server ( Kuleshov et al, 2016 ), predicts mammalian transcriptional regulators using hundreds of mammalian TF binding profiles from ENCODE ( Davis et al, 2018 ). In the plant field, the large collection of DAP-seq profiles for 529 Arabidopsis thaliana TFs ( O’Malley et al, 2016 ) is used for the enrichment analysis in web services TF DEACoN ( Harkey et al, 2020 ) and EAT-UpTF ( Shim and Seo, 2020 ).…”

“…For Arabidopsis, the enrichment tools TF DEACoN ( Harkey et al, 2020 ) and EAT-UpTF ( Shim and Seo, 2020 ) used DAP-seq peak sets from the Plant Cistrome database ( O’Malley et al, 2016 ). Here we re-processed DAP-seq raw data, getting a collection of peak sets of better quality and bigger size (peak sets for dozens of TFs were recovered).…”

Altering the balance between AOX1A and NDB2 expression affects a common set of transcripts in Arabidopsis

“…Plant Gene Ontology (GO) slim categories and in-depth biological process (BP) were evaluated and an FDR-adjusted p value < 0.05 indicates enriched GO functional categories for a given comparison. Enrichment of upstream TFs were identified using EAT-UpTF based off the relative enrichment of TFtarget genes (Shim and Seo, 2020). A FDR-adjusted p value < 0.01 indicates significantly enriched TFs in up-and downregulated DEGs.…”

CisCross web service: a gene set enrichment analysis to predict the upstream regulators for Arabidopsis thaliana

“…The large collection of similarly processed in [2] DAP-Seq sets of peaks, The Plant Cistrome database, has been used for systematic identification of TF upstream regulators [3,4]. Two webapplications for gene set enrichment analysis in Arabidopsis, TF DEACoN [4] and EAT-UpTF [5], have been developed already, which use Plant Cistrome list of TFs's targets. However, the Plant Cistrome database consists of processed by GEM tool sets of peak [2,6].…”