Effects of decitabine on 16 AML patient methylomes (CR and non-CR): significant differences in methylation level in various genomic features between day 0 (pretreatment) and day 25 (after first cycle of decitabine treatment)
| Genomic features . | CpG island associated . | Gene associated . | Total regions in genomic features* . | DMRs in genomic features . | ||
|---|---|---|---|---|---|---|
| DMRs, no. (%) total features . | Hypomethylated, no. (%) total DMRs . | Hyperrmethylated, no. (%) total DMRs . | ||||
| CpG islands | Yes | No | 27 639 | 6470 (23) | 6375 (99) | 95 (1) |
| CpG island shores | Yes | No | 55 278 | 8706 (16) | 8033 (92) | 673 (8) |
| CpG inlands | Yes | No | 55 278 | 12 571 (23) | 11 910 (95) | 661 (5) |
| Promoter-associated CpG islands | Yes | Yes | 16 393 | 1457 (11) | 1438 (99) | 19 (1) |
| Gene promoters | Partial† | Yes | 26 374 | 893 (3) | 788 (88) | 105 (12) |
| Gene deserts | No | No | 776 | 519 (67) | 20 (4) | 499 (96) |
| miRNAs | No | No | 925 | 75 (8) | 67 (89) | 8 (11) |
| miRNA-associated CpG islands | Yes | No | 68 | 20 (29) | 20 (100) | 0 |
| miRNA-associated promoters | No | No | 1051 | 86 (8) | 69 (80) | 17 (20) |
| Repeat-masked regions | No | No | 5 016 131 | 0 | 0 | 0 |
| RefSeq genes | Partial‡ | Yes | 35 430 | 10 941 (31) | 6034 (55) | 4907 (45) |
| RefSeq gene-associated CpG islands | Yes | Yes | 20 842 | 5077 (24) | 5005 (99) | 72 (1) |
| Genomic features . | CpG island associated . | Gene associated . | Total regions in genomic features* . | DMRs in genomic features . | ||
|---|---|---|---|---|---|---|
| DMRs, no. (%) total features . | Hypomethylated, no. (%) total DMRs . | Hyperrmethylated, no. (%) total DMRs . | ||||
| CpG islands | Yes | No | 27 639 | 6470 (23) | 6375 (99) | 95 (1) |
| CpG island shores | Yes | No | 55 278 | 8706 (16) | 8033 (92) | 673 (8) |
| CpG inlands | Yes | No | 55 278 | 12 571 (23) | 11 910 (95) | 661 (5) |
| Promoter-associated CpG islands | Yes | Yes | 16 393 | 1457 (11) | 1438 (99) | 19 (1) |
| Gene promoters | Partial† | Yes | 26 374 | 893 (3) | 788 (88) | 105 (12) |
| Gene deserts | No | No | 776 | 519 (67) | 20 (4) | 499 (96) |
| miRNAs | No | No | 925 | 75 (8) | 67 (89) | 8 (11) |
| miRNA-associated CpG islands | Yes | No | 68 | 20 (29) | 20 (100) | 0 |
| miRNA-associated promoters | No | No | 1051 | 86 (8) | 69 (80) | 17 (20) |
| Repeat-masked regions | No | No | 5 016 131 | 0 | 0 | 0 |
| RefSeq genes | Partial‡ | Yes | 35 430 | 10 941 (31) | 6034 (55) | 4907 (45) |
| RefSeq gene-associated CpG islands | Yes | Yes | 20 842 | 5077 (24) | 5005 (99) | 72 (1) |
CR indicates eventual complete remission; and non-CR, eventual noncomplete remission.
Total regions in genomic features with characteristics described in Table 1.
Although not explicitly named as associated with CpG islands, ∼ 43% of gene promoters are overlapped with CpG islands.
Although not explicitly named as associated with CpG islands, gene bodies and 3′UTR regions overlap with CpG islands.