Table 2 List of genes differentially methylated in the promoter region with their methylation status, genomic annotation, methylation difference, and significance
Symbol | Chromosome | DMR_start | DMR_end | Methylation difference | qvalue | Methylation status | Genomic annotation |
|---|---|---|---|---|---|---|---|
TTBK1 | Chr6 | 43,243,001 | 43,243,500 | −72.74 | 5.71E-15 | Hypo | Within TSS |
SALL1 | Chr16 | 51,151,001 | 51,151,500 | −67.04 | 2.37E-15 | Hypo | Within TSS |
DNMT3A | Chr2 | 25,252,501 | 25,253,000 | −57.11 | 1.29E-05 | Hypo | Promoter (< = 1 kb) |
LDLRAD4 | Chr18 | 13,641,501 | 13,642,000 | −49.89 | 1.00E-08 | Hypo | Within TSS |
PNMA2 | Chr8 | 26,513,501 | 26,514,000 | −47.06 | 9.83E-07 | Hypo | Within TSS |
RESP18 | Chr2 | 219,331,501 | 219,332,000 | −41.28 | 6.03E-06 | Hypo | Promoter (< = 1 kb) |
PPP1R14A | Chr19 | 38,256,001 | 38,256,500 | −40.95 | 1.65E-06 | Hypo | Within TSS |
RTKN | Chr2 | 74,442,001 | 74,442,500 | −40.77 | 8.77E-06 | Hypo | Promoter (< = 1 kb) |
ELAVL2 | Chr9 | 23,821,001 | 23,821,500 | −40.15 | 0.002342299 | Hypo | Within TSS |
ASPG | Chr14 | 104,085,501 | 104,086,000 | −40.00 | 0.005863143 | Hypo | Within TSS |
KLK7 | Chr19 | 50,984,001 | 50,984,500 | −38.50 | 4.84E-05 | Hypo | Within TSS |
STEAP1 | Chr7 | 90,153,501 | 90,154,000 | −36.54 | 7.53E-05 | Hypo | Promoter (< = 1 kb) |
HOXC5 | Chr12 | 54,031,501 | 54,032,000 | −36.44 | 0.004658024 | Hypo | Promoter (1-2 kb) |
MIR208B | Chr14 | 23,418,001 | 23,418,500 | –35.48 | 0.00010589 | Hypo | Within TSS |
OLIG3 | Chr6 | 137,494,501 | 137,495,000 | −34.62 | 0.000165504 | Hypo | Promoter (< = 1 kb) |
HTR1A | Chr5 | 63,962,501 | 63,963,000 | −32.00 | 0.000306617 | Hypo | Promoter (< = 1 kb) |
TPM2 | Chr9 | 35,693,001 | 35,693,500 | −30.80 | 0.007318167 | Hypo | Promoter (2-3 kb) |
FGFR2 | Chr10 | 121,597,001 | 121,597,500 | −28.70 | 0.000494675 | Hypo | Promoter (< = 1 kb) |
SFTPD | Chr10 | 79,983,001 | 79,983,500 | −27.50 | 0.000225499 | Hypo | Promoter (< = 1 kb) |
TMEM88B | Chr1 | 1,425,501 | 1,426,000 | −26.76 | 2.28E-05 | Hypo | Within TSS |
CRMP1 | Chr4 | 5,890,501 | 5,891,000 | −26.14 | 7.65E-05 | Hypo | Promoter (< = 1 kb) |
PHACTR3 | Chr20 | 59,583,501 | 59,584,000 | −25.00 | 1.71E-05 | Hypo | Within TSS |
TMEM176B | Chr7 | 150,801,001 | 150,801,500 | 25.71 | 2.11E-05 | Hyper | Within TSS |
EPS8 | Chr12 | 15,789,501 | 15,790,000 | 26.20 | 0.000585189 | Hyper | Promoter (< = 1 kb) |
CBLC | Chr19 | 44,777,501 | 44,778,000 | 28.37 | 0.008399354 | Hyper | Within TSS |
ARHGAP36 | ChrX | 131,082,001 | 131,082,500 | 30.00 | 0.00190226 | Hyper | Within TSS |
H1-1 | Chr6 | 26,017,501 | 26,018,000 | 30.91 | 3.63E-05 | Hyper | Within TSS |
FRRS1L | Chr9 | 109,167,001 | 109,167,500 | 31.03 | 1.81E-06 | Hyper | Within TSS |
DOK7 | Chr4 | 3,476,001 | 3,476,500 | 33.09 | 0.001766174 | Hyper | Within TSS |
SRGAP1 | Chr12 | 63,843,001 | 63,843,500 | 33.93 | 0.00895754 | Hyper | Promoter (1-2Â kb) |
CLDN6 | Chr16 | 3,018,501 | 3,019,000 | 36.88 | 0.003000378 | Hyper | Promoter (< = 1 kb) |
EMILIN3 | Chr20 | 41,367,001 | 41,367,500 | 38.10 | 8.11E-05 | Hyper | Promoter (< = 1 kb) |
CDH4 | Chr20 | 61,599,501 | 61,600,000 | 48.00 | 6.69E-05 | Hyper | Within TSS |
GORAB | Chr1 | 170,531,001 | 170,531,500 | 49.50 | 1.68E-05 | Hyper | Promoter (< = 1 kb) |
KLK1 | Chr19 | 50,826,501 | 50,827,000 | 54.00 | 0.000165918 | Hyper | Promoter (2-3Â kb) |
GNAL | Chr18 | 11,751,001 | 11,751,500 | 54.53 | 4.63E-12 | Hyper | Within TSS |
AUTS2 | Chr7 | 70,693,501 | 70,694,000 | 60.61 | 4.18E-12 | Hyper | Promoter (< = 1 kb) |
FANK1 | Chr10 | 125,896,501 | 125,897,000 | 61.84 | 2.87E-10 | Hyper | Within TSS |
DPEP3 | Chr16 | 67,980,001 | 67,980,500 | 64.01 | 4.73E-10 | Hyper | Within TSS |
CDKL4 | Chr2 | 39,245,001 | 39,245,500 | 68.97 | 7.32E-14 | Hyper | Promoter (1-2Â kb) |
RSPH14 | Chr22 | 23,181,501 | 23,182,000 | 69.70 | 3.33E-17 | Hyper | Promoter (< = 1 kb) |