Genome-wide computational prediction of transcriptional regulatory modules reveals new insights into human gene expression

Overview of the CRM prediction algorithm. TFBS predictions for different PWMs are shown with different geometric shapes and their size indicates the score of the hit. Hits from individual species are combined using a weighted average method to compute the “Aligned hits.” The most significant (up to five) aligned hits are considered as “Tags” for the corresponding region. The sum of the Tags scores is used to calculate a “Module score” using a statistical significance estimation. This operation is performed for each position of the human genome, for sliding windows of size 100, 200, 500, 1000, and 2000 bp.