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: Supplementary information: Supplementary material is available at Bioinformatics online. © 2013 The Author(s) 2013. Published by Oxford University Press.
CITATION STYLE
Auerbach, R. K., Chen, B., & Butte, A. J. (2013). Relating genes to function: Identifying enriched transcription factors using the ENCODE ChIP-Seq significance tool. Bioinformatics, 29(15), 1922–1924. https://doi.org/10.1093/bioinformatics/btt316
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