MotifExpress is a tool for rapidly discovering cis-regulatory motifs by correlating sequence to expression data. It will discover motifs whose presence is best correlated with changes in genome-wide gene expression from a control state to an experimental state. It uses expression data as measured by microarray or RNA-seq, and repeatmasked sequence data from regions relevant to the genes whose expression has been measured.
MotifExpress was designed for win32 systems, and requires a number of prerequisites to function. You should download them first, if you do not have them:
- Python 2.5+
- R 2.6.2
Download MotifExpress here.
MotifExpress was developed by Leonid Zamdborg and Ping Ma at the Institute for Genomic Biology, University of Illinois at Urbana-Champaign. It incorporates code written by Erin M. Conlon and X. Shirley Liu (MDScan), Berwin Turlach (SVS), Leonard Richardson (BeautifulSoup), and the Cygwin Project.
Please contact Ping Ma with any questions, comments, or bug reports.