Figure 2 illustrates an example of the predicted CRMs for the eye-specific gene BFSP1 (RefSeq ID: NM_001195; UniGene ID: Hs.129702; Ensembl ID: ENSG00000125864). We show the evolutionary conservation, TF binding site density, and potential energy in the plot. The density was calculated by counting the number of all known TFBS in a sliding window (200 bp). The conservation score was obtained from UCSC genome database [15,16]. The transcription start site (TSS) is based on RefSeq. By comparing the conservation and energy profile, we can see that the predicted cis-regulatory modules are not always located in conserved regions. Also, the discrepancy in the density and energy profiles implies the importance of identifying the sets of relevant TFs.
