Table 1.
p-values of methylation-mediated features in cancer DNAm data obtained from BeadChip GEO data series.
| GEO ID | Cancer Data Series | Samples | Assay | DMS(+/−) | G + C/ΟΕ CpG content | G4 | Pals | Alt. Spl. | TFBS | cTFBS | Ref | |||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| mean(sd) | p-val | mean(sd) | p-val | p-val | mean(sd) | p-val | mean(sd) | p-val | mean(sd) | |||||||
| GSE42752 | Colorectal adenocarcinoma | 22/22 | HM450k | 2,028 | 0.68/0.83 | 2.90 (1.33) | <10−3 | 9.65 (4.63) | 0.002 | — | 0.07 (0.25) | 0.065 | 5.96 (5.81) | 0.23 | 0.35 (1.17) | 71 |
| 49 | 0.55/0.52 | 1.51 (1.10) | 7.53 (3.11) | — | 9.25 (4.19) | 0.2 (0.91) | ||||||||||
| GSE54503 | Hepatocellular carcinoma | 66/66 | HM450k | 1,227 | 0.69/0.85 | 2.87 (1.37) | <10−3 | 10.43 (5.03) | <10−3 | <10−3 | 0.07 (0.25) | 0.143 | 5.61 (5.07) | <10−3 | 0.38 (1.16) | 51 |
| 7,490 | 0.53/0.52 | 1.18 (1.19) | 6.9 (3.06) | 0.01 (0.08) | 6.62 (6.52) | 0.08 (0.5) | ||||||||||
| GSE85464* | Gastric adenocarcinoma | 19/19 | HM450k | 161 | 0.65/0.78 | 2.57 (1.37) | <10−3 | 8.95 (4.94) | <10−3 | — | 0.08 (0.27) | 0.002 | 5.06 (4.82) | <10−3 | 0.4 (1.13) | 72 |
| 353 | 0.53/0.57 | 1.25 (1.24) | 6.9 (3.4) | — | 11.25 (14.29) | 0.1 (0.66) | ||||||||||
| GSE25093 | Head & NeckSC carcinoma | 91/18 | HM27k | 16 | 0.60/0.68 | 1.69 (1.13) | 0.188 | 8.12 (4.96) | 0.56 | 0.423 | 0.06 (0.25) | 0.481 | 12 (12.19) | 0.28 | 0.81 (2.74) | 73 |
| 83 | 0.53/0.4 | 1.29 (1.04) | 7.06 (3.18) | 0.02 (0.15) | 9.32 (11.9) | 0.16 (0.63) | ||||||||||
| GSE32866* | Lung adenocarcinoma | 28/27 | HM27k | 175 | 0.66/0.82 | 2.45 (1.35) | <10−3 | 9.78 (4.62) | <10−3 | 0.941 | 0.04 (0.20) | 0.443 | 5.73 (5.1) | 0.174 | 0.63 (1.56) | 74 |
| 23 | 0.53/0.35 | 1.17 (1.27) | 5.26 (2.07) | 0.04 (0.21) | 9.67 (8.96) | 0.13 (0.34) | ||||||||||
| GSE37754# | Breast cancer | 62/10 | HM450k | 152 | 0.59/0.69 | 1.95 (1.39) | <10−3 | 7.25 (2.72) | 0.466 | — | 0.03 (0.18) | 0.546 | 5.67 (9.54) | 0.36 | 0.24 (0.92) | 75 |
| 49 | 0.48/0.39 | 1.02 (1.13) | 6.9 (3.1) | — | 4.83 (3.19) | 0.1 (0.42) | ||||||||||
| GSE26989 | Ovarian cancer | 41/10 | HM27k | 613 | 0.56/0.49 | 1.54 (1.34) | 0.001 | 7.12 (3.52) | 0.099 | 0.304 | 0.09 (0.29) | 0.751 | 7.98 (9.56) | 0.008 | 0.32 (1.17) | 76 |
| 1,160 | 0.53/0.38 | 1.31 (1.21) | 6.84 (3.11) | 0.08 (0.27) | 7.57 (7.93) | 0.18 (0.69) | ||||||||||
| GSE109402 | Medulloblastoma | 33/5 | EPIC | 14,120 | 0.55/0.43 | 1.22 (1.19) | <10−3 | 7.23 (3.25) | 0.0095 | 0.002 | 0.04 (0.19) | 0.121 | 6.1 (5.76) | 0.0099 | 0.16 (0.72) | 77 |
| 56,444 | 0.48/0.32 | 0.95 (1.09) | 6.86 (3.09) | 0.01 (0.12) | 7.83 (8.29) | 0.08 (0.53) | ||||||||||
| GSE61441 | Renal cell carcinoma | 46/46 | HM450k | 86 | 0.60/0.74 | 1.97 (1.52) | <10−3 | 8.2 (3.53) | 0.002 | 0.36 | 0.03 (0.18) | 0.95 | 4.64 (2.62) | 0.002 | 0.36 (0.94) | 78 |
| 129 | 0.50/0.35 | 1.15 (1.21) | 6.78 (2.97) | 0.02 (0.12) | 5.69 (5.84) | 0.09 (0.64) | ||||||||||
DMS+ and DMS− columns contain the number of hypermethylated and hypomethylated sites (DMS) respectively, for various cancer datasets (Cancer Data Series) and BeadChip assays. Maximum 1,000 sites were analyzed. p-values (p-val columns) are calculated with t-test and Wilcoxon test for non-normal distributions in addition to the mean values and standard deviations for each feature (mean(sd) columns). Column G + C/OE CpG content contains the G + C content and the observed/expected (OE) ratio of the CpG frequencies. Putative transcription factor binding sites (TFBS column) were identified only in DMS sequences located in promoters. The samples column contains the number of tumor/normal samples included from each data series (matched pairs when numbers are identical). p-values are not shown when no DMS co-localized with alternative splicing events (Alt. Spl column). *|Δβ| > 0.25, #transformed M-values, |Δβ| > 0.20. G4: G-quadruplexes, Pals: Palindromes, cTFBS: Conserved TFBS, SC: squamous cell.