Cancer Institute A national cancer institute
designated cancer center

Atul Butte

Publication Details

  • Relating Genes to Function: Identifying Enriched Transcription Factors using the ENCODE ChIP-Seq Significance Tool. Bioinformatics (Oxford, England) Auerbach, R. K., Chen, B., Butte, A. J. 2013


    MOTIVATION: Biological analysis has shifted from identifying genes to mapping these genes to biological function. 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

    View details for PubMedID 23732275

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