Table 5. .
Correlation between Detected Hotspot Positions and Genomic Features in the HapMap ENCODE Regions
| Mean Occurrence or Average Value |
||||
| Feature | In Putative Hotspots | In Random Hotspots | Enriched or Depleted in Putative Hotspots |
P |
| Basic sequence features: | ||||
| G+C content | .432 | .400 | Enriched | <.0001 |
| No. of CpG islands | 10 | 7.78 | … | .2587 |
| Genomic repeatsa: | ||||
| All families of repeats | .396 | .456 | Depleted | .0014 |
| Alu | 143 | 156.5 | … | .2175 |
| L1 | 117 | 149.7 | Depleted | .0143 |
| MIR | 118 | 90.1 | Enriched | .0061 |
| Simple_repeat | 78 | 63.9 | … | .0671 |
| L2 | 90 | 63.9 | Enriched | .0041 |
| Low_complexity | 77 | 57.7 | Enriched | .0180 |
| MaLR | 56 | 50.2 | … | .2532 |
| RefSeq genes and related features: | ||||
| Gene regionsb | .2790 | .3913 | Depleted | .0009 |
| Exonic bases | .0244 | .0228 | … | .3863 |
| UTRs (5′ + 3′) | .0089 | .0127 | … | .3288 |
| DHSSs: | ||||
| Sites in DNase GM069 Chip | 26 | 13.1 | Enriched | .0031 |
| Sites in DNase CD4 Chip | 24 | 13.0 | Enriched | .0185 |
| Sites in DNase CD4 MPSS | 4 | 2.5 | … | .2445 |
| Sites in DNase CD4-act MPSS | 4 | 2.7 | … | .2889 |
a
Only families of repeats that occur >500 times in the studied regions are listed here. All other repeat families are not tested significantly related with the hotspots.
b
Gene regions are calculated as 1 kb upstream of the first exon to 1 kb downstream from the last exon.