Table I.
The top 20 significant differentially methylated genes (DMGs) with CpGs between bad prognostic group and good prognostic group sorted according to false discovery rate (FDR).
| Methylation loci | Chr. | Position | Genes | Location | β-bad | β-good | Effect | Pnominal | FDR |
|---|---|---|---|---|---|---|---|---|---|
| cg03904042 | chr20 | 31719152 | NECAB3 | Body | 0.3413 | 0.2296 | −0.5719 | 8.05×10−7 | 2.21×10−5 |
| cg04488521 | chr5 | 178420322 | ZNF354C | Promoter | 0.3382 | 0.2272 | −0.5737 | 3.42×10−6 | 9.37×10−5 |
| cg09595479 | chr12 | 47975479 | PRPH | 1stExon | 0.4229 | 0.3151 | −0.4244 | 5.31×10−6 | 1.45×10−4 |
| cg00054702 | chr5 | 135556442 | LOC389332 | Body | 0.1967 | 0.1149 | −0.7755 | 8.34×10−6 | 2.29×10−4 |
| cg07040405 | chr2 | 174537121 | SP3 | Promoter | 0.0306 | 0.0383 | 0.3253 | 9.43×10−6 | 2.59×10−4 |
| cg13146839 | chr3 | 192063116 | LOC647309 | 1stExon | 0.4032 | 0.5159 | 0.3556 | 1.12×10−5 | 3.08×10−4 |
| cg00741900 | chr14 | 101097550 | DIO3 | 5′UTR | 0.3288 | 0.2510 | −0.3892 | 1.15×10−5 | 3.14×10−4 |
| cg27229100 | chr20 | 47330667 | C20orf199 | Body | 0.4259 | 0.5299 | 0.3153 | 1.44×10−5 | 3.94×10−4 |
| cg13316171 | chr2 | 187059280 | ZC3H15 | 1stExon | 0.0212 | 0.0273 | 0.3649 | 1.56×10−5 | 4.28×10−4 |
| cg01494348 | chr8 | 144731538 | NAPRT1 | Promoter | 0.1567 | 0.0991 | −0.6612 | 1.64×10−5 | 4.50×10−4 |
| cg24960763 | chr12 | 132217389 | ZNF10 | Promoter | 0.0867 | 0.0578 | −0.5848 | 1.90×10−5 | 5.22×10−4 |
| cg18113994 | chr19 | 62817679 | ZNF134 | 1stExon | 0.0784 | 0.1796 | 1.1953 | 2.04×10−5 | 5.60×10−4 |
| cg06815419 | chr15 | 81526866 | BTBD1 | Promoter | 0.0215 | 0.0265 | 0.3018 | 2.05×10−5 | 5.63×10−4 |
| cg25019777 | chr4 | 53220160 | USP46 | Promoter | 0.0432 | 0.0641 | 0.5716 | 2.08×10−5 | 5.70×10−4 |
| cg00004421 | chr17 | 7415803 | SENP3 | TSS1500 | 0.4066 | 0.4947 | 0.2828 | 2.35×10−5 | 6.44×10−4 |
| cg01331992 | chr9 | 19369118 | RPS6 | Body | 0.2316 | 0.3035 | 0.3899 | 2.95×10−5 | 8.09×10−4 |
| cg00767496 | chr15 | 43458571 | GATM | Body | 0.5105 | 0.4140 | −0.3020 | 3.00×10−5 | 8.22×10−4 |
| cg21858255 | chr12 | 103133739 | TXNRD1 | Promoter | 0.1570 | 0.0696 | −1.1737 | 3.15×10−5 | 8.64×10−4 |
| cg02605461 | chr20 | 32047137 | RALY | 5′UTR | 0.3931 | 0.4871 | 0.3095 | 3.37×10−5 | 9.25×10−4 |
| cg26658728 | chr16 | 65195711 | CMTM3 | 5′UTR | 0.1783 | 0.1032 | −0.7891 | 3.38×10−5 | 9.26×10−4 |
The first column indicates the cg number of the methylation site; the second column indicates the chromosome number of detected methylation site; the third column indicates the chromosome position of the detected methylation site; the fourth column indicates the gene name of methylation area; the fifth column represents the CpGs location in methylation regional; the sixth and seventh columns represent the average methylation level β of CpGs in bad and good prognostic groups; the eighth column represents log2FC (good/bad); the ninth column represents the P-value; and the tenth column represents the corrected FDR value.