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Updated: May 10, 2026

Mapping the Structure-Function Relationships of Disordered Oncogenic Transcription Factors Using Transcriptomic Analysis
Published on: June 27, 2020
Relating genes to function: identifying enriched transcription factors using the ENCODE ChIP-Seq significance tool
Raymond K Auerbach1, Bin Chen, Atul J Butte
1Division of Systems Medicine, Department of Pediatrics, Stanford University School of Medicine, 1265 Welch Road, Room X-163 MS-5415, Stanford, CA 94305, USA.
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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