title: Relating genes to function: identifying enriched transcription factors using the ENCODE ChIP-Seq significance tool.
abstract: BACKGROUND
  Biological analysis has shifted from identifying genes and transcripts to mapping these genes and transcripts to biological functions. The ENCODE Project has generated hundreds of ChIP-Seq experiments spanning multiple transcription factors and cell lines for public use, but tools for a biomedical scientist to analyze these data are either non-existent or tailored to narrow biological questions. We present the ENCODE ChIP-Seq Significance Tool, a flexible web application leveraging public ENCODE data to identify enriched transcription factors in a gene or transcript list for comparative analyses.
  
  
  METHODS
  The ENCODE ChIP-Seq Significance Tool is written in JavaScript on the client side and has been tested on Google Chrome, Apple Safari and Mozilla Firefox browsers. Server-side scripts are written in PHP and leverage R and a MySQL database. The tool is available at http://encodeqt.stanford.edu.
  
  
  BACKGROUND
  abutte@stanford.edu
  
  
  BACKGROUND
  Supplementary material is available at Bioinformatics online.
authors.affiliation: Division of Systems Medicine, Department of Pediatrics, Stanford University School of Medicine, 1265 Welch Road, Room X-163 MS-5415, Stanford, CA 94305, USA.
authors.forename: Raymond K
authors.initials: RK
authors.lastname: Auerbach
authors.forename: Bin
authors.initials: B
authors.lastname: Chen
authors.forename: Atul J
authors.initials: AJ
authors.lastname: Butte
mesh_terms: D047369:Chromatin Immunoprecipitation; D005796:Genes; D020407:Internet; D017422:Sequence Analysis, DNA; D012984:Software; D014157:Transcription Factors / Q000378:metabolism*
chemical_list: D014157:Transcription Factors