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. 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

Raymond K Auerbach  1 , Bin Chen, Atul J Butte
Affiliations

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

Raymond K Auerbach et al. Bioinformatics. .

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.

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Figures

Fig. 1.
Fig. 1.
The ENCODE ChIP-Seq significance tool after a query
See this image and copyright information in PMC

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