Mar 23, 2020

EAT-UpTF: Enrichment Analysis Tool for Upstream Transcription Factors of a gene group

BioRxiv : the Preprint Server for Biology
S. Shim, Pil Joon Seo

Abstract

EAT-UpTF (Enrichment Analysis Tool for Upstream Transcription Factors of a gene group) 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. Contactsangreashim@gmail.com or pjseo1@snu.ac.kr Availabilityhttps://github.com/sangreashim/EAT-UpTF

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Mentioned in this Paper

Vaccines
Influenza virus vaccine
Influenza
Influenza A virus
Trivalent influenza vaccine
Antiviral Therapy
Conservative Therapy
Population Group
Urban Population
Antiviral Agents

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