Table 4.

Enrichment and depletion of annotated genomic features in active and repressed domains based on the four-track simultaneous segmentation

Column 1 indicates genomic annotations based on genes and transcripts, CpG islands, repetitive elements, and evolutionary conservation. Rows 1–3: Total number of GENCODE transcriptional start sites, mRNA 5′ ends, and 5′ ends of spliced ESTs. Row 4: Total percent of bases overlapped by all ESTs (spliced and unspliced). Total ESTs. Row 5: Total percent of bases overlapped by CpG islands. Rows 6–12: Total percent of bases overlapped by all repetitive elements; DNA repeats; L1 LINEs; L2 LINEs; LTR elements; Alu SINEs; and simple repetitive sequences. Rows 13–15: Total percent of bases overlapped by different stringencies (strict, moderate, loose) of conserved sequence elements identified by the ENCODE MSA group. Row 16: Percent bases overlapped by nonexonic noncoding MSA conserved sequences at moderate stringency (=MSA moderate minus GENCODE exons). Columns 2–3 contain the number of elements (or the number of bases of each element) in each state, with the fraction of the total in parentheses. Columns 4–9 show the relative proportion of enrichment or depletion of the element within each state over the expected value, the corresponding P-values, and an adjusted P-value. P-values and adjusted P-values are computed via permutation of the state labels using 10,000 iterations (see Methods).