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Bioinformatics. 2013 Aug 1;29(15):1922-4. doi: 10.1093/bioinformatics/btt316. Epub 2013 Jun 3.

Relating genes to function: identifying enriched transcription factors using the ENCODE ChIP-Seq significance tool.

Author information

1
Division of Systems Medicine, Department of Pediatrics, Stanford University School of Medicine, 1265 Welch Road, Room X-163 MS-5415, Stanford, CA 94305, USA.

Abstract

MOTIVATION:

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.

IMPLEMENTATION:

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.

CONTACT:

abutte@stanford.edu

SUPPLEMENTARY INFORMATION:

Supplementary material is available at Bioinformatics online.

PMID:
23732275
PMCID:
PMC3712221
DOI:
10.1093/bioinformatics/btt316
[Indexed for MEDLINE]
Free PMC Article

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