Table 1.
The combinatorial patterns benchmarked against the canonical states reported in Ernst and Kellis
| Group in EK | EK states | iHMM | scHMM | Difference | Window region |
|---|---|---|---|---|---|
| Promoter | Promoter upstream (1–3) | 15 467 | 14 543 | −924 | Promoter |
| Repressed promoter (4) | 5275 | 52 435 | −323 | (±500 bp around TSS) | |
| TSS (5–7) | 19 918 | 21 813 | 1895 | (±500 bp around TSS) | |
| Transcribed promoter (8–11) | 1157 | 1506 | 349 | ||
| Unmappable | 7082 | 6085 | −997 | ||
| Transcribed | Transcribed 5′ proximal (12–16) | 20 760 | 172 887 | 152 127 | Gene body (TSS to TES) |
| Transcribed less 5′ proximal (17–19) | 116 328 | 247 765 | 131 437 | ||
| Candidate strong enhancer in transcribed regions (20) | 17 970 | 19 342 | 1372 | ||
| Spliced exons/GC rich (21–23) | 374 693 | 367 132 | −7561 | ||
| Transcribed 5′ distal (24–26) | 3 574 145 | 3 290 702 | −283 443 | ||
| End of transcription; exons (27) | 30 694 | 40 831 | 10 137 | ||
| ZNF genes; Krüppel-associated protein repressed state (28) | 25 901 | 29 955 | 4054 | ||
| Unmappable | 104 953 | 96 830 | −8123 | ||
| Active intergenic | Candidate strong distal enhancer (29–30) | 4794 | 3641 | −1153 | 5′ Proximal, intergenic (2 kb to 500 bp upstream of TSS) |
| Intergenic H2AZ with open chr/transcription factor binding (31) | 1362 | 1640 | 278 | ||
| Candidate distal enhancer (32–33) | 22 468 | 22 325 | −143 | ||
| Proximal to active enhancers (34) | 33 137 | 49 639 | 16 502 | ||
| Active intergenic regions (35–36) | 17 724 | 44 029 | 26 305 | ||
| Non-repressive intergenic domains (37) | 503 737 | 460 364 | −43 373 | ||
| H2AZ-specific state (38) | 4788 | 6124 | 1336 | ||
| CTCF island; candidate insulator (39) | 3388 | 3549 | −161 | ||
| Unmappable | 16 766 | 16 026 | −741 | ||
| Repressed | Unmappable (40) | 7 356 220 | 4 913 502 | −2 442 718 | Intergenic (10 kb away from gene body) |
| Heterochromatin (Heterochr); nuclear lamina (41–42) | 80 171 | 1 100 873 | 1 020 702 | ||
| Heterochr; lower gene depletion (43–44) | 259 095 | 979 003 | 719 908 | ||
| Specific repression (45) | 145 073 | 389 647 | 244 574 | ||
| Unmappable | 18 492 | 18 759 | 87 | ||
| Repetitive | Simple repeats (CA)n, (TG)n (46) | 56 231 | 54 950 | −1281 | Intergenic (10 kb away from gene body) |
| L1/long terminal repeats (47) | 54 692 | 393 782 | 339 090 | ||
| Satellite repeat (48–51) | 49 967 | 172 446 | 122 479 | ||
| Unmappable | 70 395 | 67 641 | −2754 |