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 e

SUBMITTER: Shim S 

PROVIDER: S-EPMC7516213 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature