Relating genes to function: identifying enriched transcription factors using the ENCODE ChIP-Seq significance tool
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- Raymond K. Auerbach
- Division of Systems Medicine, Department of Pediatrics, Stanford University School of Medicine, 1265 Welch Road, Room X-163 MS-5415, Stanford, CA 94305, USA
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- Bin Chen
- Division of Systems Medicine, Department of Pediatrics, Stanford University School of Medicine, 1265 Welch Road, Room X-163 MS-5415, Stanford, CA 94305, USA
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- Atul J. Butte
- Division of Systems Medicine, Department of Pediatrics, Stanford University School of Medicine, 1265 Welch Road, Room X-163 MS-5415, Stanford, CA 94305, USA
抄録
<jats:title>Abstract</jats:title> <jats:p>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.</jats:p> <jats:p>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.</jats:p> <jats:p>Contact: abutte@stanford.edu</jats:p> <jats:p>Supplementary information: Supplementary material is available at Bioinformatics online.</jats:p>
収録刊行物
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- Bioinformatics
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Bioinformatics 29 (15), 1922-1924, 2013-06-03
Oxford University Press (OUP)