Tuesday, June 4, 2013

Fwd: Relating Genes to Function: Identifying Enriched Transcription Factors using the ENCODE ChIP-Seq Significance Tool

It is strongly advised to listen first to Raymond Auerbach's webcast on YouTube: http://www.youtube.com/watch?v=kMpjiaIfWs8

Fwd: please follow footer link

Relating Genes to Function: Identifying Enriched Transcription Factors using the ENCODE ChIP-Seq Significance Tool: "

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 http://encodeqt.stanford.edu.

(Via Bioinformatics - Advance Access.)