Purpose:
Motif scanning of gene promoter regions is commonly used to determine which genes are regulated by a particular transcription factor (TF). Unlike the processes of genetic regulation, motif scanning is not tissue-specific, resulting in many false positive predictions of regulation. This problem can greatly decrease the accuracy the many different analyses that use in silico TF binding site predictions in specific tissues.
DR Gene integrates tissue-specific histone modification information with PWM scanning. In our testing, our DR Gene makes only approximately half as many false positive errors as traditional methods. You can read more about our software and testing in the paper.
Get it:
The tool and the data used in the paper are currently available for download as source for both Mac OS X and Unix from the download page.