Table 3.
Lists of significant biological functions among the genomic regions that include 2,199 differentially methylated CpG positions between baseline (prior to their receipt of chemotherapy [T1]) and one year after the initiation of chemotherapy (T4).
| Biological Process | Hyper rank | Hyper raw P-value | Hyper FDR Q-value |
Hyper fold enrichment |
Hyper total regions |
Hyper foreground gene hits | Total genes annotated | Genes |
|---|---|---|---|---|---|---|---|---|
| Negative regulation of cytoplasmic mRNA processing body assembly | 1 | 9.2158 × 10−7 | 9.6213 × 10−3 | 132.4726 | 5 | 1 | 1 | PATL2 |
| Regulation of interleukin-8 production | 6 | 2.3100 × 10−5 | 4.0193 × 10−2 | 2.8012 | 1734 | 11 | 43 | TLR5, BCL10, TNF, AFAP1L2, WNT5A, F2RL1, TLR4, GDF2, NLRP10, ARRB1 |
| Dimethylallyl diphosphate biosynthetic process | 9 | 3.9826 × 10−5 | 4.6198 × 10−2 | 4.5804 | 530 | 1 | 2 | IDI1 |
| Positive regulation of chemokine biosynthetic process | 13 | 5.2148 × 10−5 | 4.1879 × 10−2 | 4.8847 | 452 | 5 | 10 | TNF, MYD88, WNT5A, IL4, IFNG |
| Regulation of cellular senescence | 14 | 5.3600 × 10−5 | 3.9970 × 10−2 | 3.5942 | 860 | 7 | 12 | CDK6, NUAK1, VASH1, HMGA1, ZKSCAN3, NEK6, HMGA2 |
Abbreviations: AFAP1L2, actin filament associated protein 1 like 2; ARRB1, arrestin beta 1; BCL10, B-cell lymphoma/leukaemia 10; CDK6, cyclin-dependent kinase 6; F2RL1, coagulation factor II (thrombin) receptor-like 1; FDR, false discovery rate; GDF2, growth differentiation factor 2; HMGA1, high mobility group AT-hook 1; HMGA2, high mobility group AT-hook 2; IDI1, isopentenyl-diphosphate delta isomerase 1; IFNG, interferon gamma; IL4, interleukin 4; MYD88, myeloid differentiation primary response 88; NEK6, never in mitosis gene a (NIMA)-related kinase 6; NLRP10, nucleotide-binding oligomerization domain (NOD)-like receptor family pyrin domain containing 10; NUAK1, novel (nua) kinase family 1; PATL2, protein associated with topoisomerase 2; TLR4, toll like receptor 4; TLR5, toll like receptor 5; TNF, tumour necrosis factor; VASH1, vasohibin 1; WNT5A, Wnt family member 5A; ZKSCAN3, zinc-finger with Kruppel-associated box (KRAB) and soluble calcium-activated nucleotidase (SCAN) domains.