Figure 5.

Distribution of distance to transcription start site for CNSs and predicted CRMs. (a) All human-mouse conserved noncoding sequences (CNSs) in transcription factor binding site (TFBS) sets 1 and 2 (both are based on the same set of CNSs) and in TFBS set 3. (b) The distribution from panel (a), when divided into six unequal bins. (c) Distribution of all CNSs upstream of genes within the microarray clusters (of genes expressed in different adult tissues) and the embryonic development gene sets, where CRMs could successfully be detected (Tables 2 and 3), divided into the same six bins as under panel (b). (d) Distribution of the distance to transcription start for the CRMs that ModuleMiner identified near to the genes from panel (c). (e) Distribution of distance to transcription start for the CRMs that ModuleMiner identified in a whole genome scan (genes in panel (d) were removed, such that only new target genes where represented here). Note that panels (b) to (e) are drawn to the same scale. (f) Portion of CNSs near to the genes in the different microarray clusters and embryonic development sets that is located within 200 base pairs (bp) of the transcription start site. (g) Portion of predicted CRMs near to the genes in the different microarray clusters and embryonic development sets that is located within 200 bp of the transcription start site. (h) Portion of CRMs predicted in a whole-genome scan for the transcriptional regulatory global model built for the different gene sets that is located within 200 bp of the transcription start site. The blue line in panels (f) to (h) indicates the portion of all CNSs (within 10 kilobases 5' of all human genes) that is less then 200 base pairs of the transcription start site. CI, Confidence Interval.