Table 3.
Association of differential H3K27ac and H3K4me3 occupancy with differential gene expression.
| Mark | Region | Differential peaks | Non-differential peaks | Enrichment | |||
|---|---|---|---|---|---|---|---|
| Type | Total | Linked to up-regulated gene | Total | Linked to up-regulated gene | |||
| H3K27ac | > TSS ± 2.5 kb | Up in normal | 5462 | 1001 (265) | 35,788 | 1372 (323) | 4.78 |
| H3K27ac | > TSS ± 2.5 kb | Up in T-PLL | 2833 | 583 (167) | 35,788 | 1112 (287) | 6.62 |
| H3K27ac | ≤ TSS ± 2.5 kb | Up in normal | 524 | 212 (136) | 16,866 | 355 (213) | 19.22 |
| H3K27ac | ≤ TSS ± 2.5 kb | Up in T-PLL | 543 | 166 (123) | 16,866 | 270 (187) | 19.1 |
| H3K4me3 | > TSS ± 2.0 kb | Up in normal | 1959 | 272 (175) | 17,596 | 635 (321) | 3.83 |
| H3K4me3 | > TSS ± 2.0 kb | Up in T-PLL | 1086 | 165 (102) | 17,596 | 626 (300) | 4.27 |
| H3K4me3 | ≤ TSS ± 2.0 kb | Up in normal | 742 | 212 (186) | 15,775 | 471 (403) | 9.57 |
| H3K4me3 | ≤ TSS ± 2.0 kb | Up in T-PLL | 148 | 85 (84) | 15,775 | 509 (394) | 17.8 |
Total RNA-seq differential expression analysis and ChIP-seq DiffBind were performed on four T-PLL (P1, P3, P5 and P6) and three normal (N1-N3). Peaks were split into those that showed differential occupancy between T-PLL and normal and others that showed no differential occupancy based on DiffBind analysis (FDR ≤ 0.05, fold-change ≥ 2). Peaks were assigned to the nearest genes. For differential peaks showing increased occupancy in normal (“Up in normal”), the number in parentheses indicates the number of up-regulated genes in normal. For differential peaks showing increased occupancy in T-PLL (“Up in T-PLL”), the number in parentheses indicates the number of up-regulated genes in T-PLL. Enrichment level is estimated as: (Number of differential peaks linked to differentially-expressed genes/total differential peaks) / (Number of non-differential peaks linked to differentially-expressed genes/total non-differential peaks).