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Table 2 Multivariate Cox proportional hazard model analyses of associations between alternative exons, methylation of corresponding CpG and cancer patients’ survival

From: Genome-wide analysis reveals the association between alternative splicing and DNA methylation across human solid tumors

Tumor type Gene expression PSI Methylation level
Gene P HR(95%CI) Alternative Exon P HR(95%CI) CpGs P HR(95%CI)
BRAC FAXDC2 0.558 0.96 (0.84,1.10) 3 0.036 3.98 (1.09,0.04) cg18260397 0.428 0.57 (0.14,2.31)
COAD OBSCN 0.753 0.97 (0.78,1.20) 118 0.001 0.20 (0.20,0.08) cg25318301 0.380 0.48 (0.09,2.49)
        cg03669282 0.581 0.72 (0.23,2.31)
HNSC ABL2 0.489 1.10 (0.84,1.42) 2 0.020 4.59 (1.27,16.58) cg03471346 0.095 0.40 (0.14,1.17)
HNSC DNASE1L1 0.003 1.45 (1.13,1.86) 3.1 0.007 4.40 (1.49,12.95) cg21459545 0.788 0.84 (0.25,2.90)
HNSC RARA 0.393 1.16 (0.82,1.63) 5 0.009 0.08 (0.01,0.54) cg05824218 0.350 1.93 (0.49,7.64)
KIRC ATG16L2 0.104 1.14 (0.97,0.10) 4.1:4.2 0.011 6.79 (1.55,29.83) cg21806242 0.187 13.92 (0.28,698.07)
KIRC EGFLAM 0.957 1.00 (0.85,1.17) 20.1 0.047 0.43 (0.18,0.99) cg21201393 0.197 4.73 (0.45,50.22)
KIRC EVL 0.004 1.47 (1.13,1.90) 3 0.027 0.32 (0.12,0.88) cg18621299 0.885 0.84 (0.07,9.47)
KIRC FMNL1 0.318 1.13 (0.89,1.42) 13.1 0.010 3.59 (1.37,9.44) cg19735250 0.261 2.95 (0.45,19.42)
KIRC NAV2 0.276 1.17 (0.88,1.54) 17 0.014 96.94 (2.48,3787.07) cg19222784 0.857 0.82 (0.10,6.76)
        cg20949700 0.997 1.00 (0.13,7.54)
KIRC SIGIRR 0.668 1.06 (0.80,1.40) 2 0.041 6.29 (1.08,36.63) cg02585906 0.173 0.24 (0.03,1.88)
        cg23029021 0.005 0.08 (0.01,0.47)
KIRC TBC1D14 0.908 0.98 (0.65,1.46) 4 0.024 26.17 (1.52,449.63) cg16851482 0.778 1.44 (0.12,17.83)
KIRC ZNF577 0.975 1.00 (0.82,1.22) 1.2:1.3 0.009 6.05 (1.57,23.33) cg03562414 0.471 1.59 (0.45,5.62)
        cg10635122 0.320 2.03 (0.50,8.22)
        cg11269599 0.007 7.39 (1.74,31.47)
        cg10783469 0.214 2.73 (0.56,13.32)
        cg16731240 0.030 4.41 (1.16,16.78)
        cg23010048 0.053 4.04 (0.98,16.61)
        cg24794228 0.228 2.28 (0.60,8.69)
KIRP C19orf25 0.012 0.50 (0.29,0.86) 2.4 0.006 0.01 (0.00,0.26) cg16613938 0.665 0.55 (0.04,8.14)
        cg23291200 0.980 0.94 (0.01,163.12)
KIRP CABP1 0.0004 0.72 (0.60,0.87) 3.1 0.004 59.40 (3.63,972.14) cg24292016 0.011 0.02 (0.00,0.42)
        cg25969992 0.011 0.04 (0.00,0.49)
KIRP CALD1 0.632 0.88 (0.52,1.49) 2 0.013 8.85 (1.58,49.62) cg04874031 0.007 149.57 (3.97,5636.65)
        cg16253634 0.019 148.62 (2.24,9849.90)
        cg24956866 0.027 97.96 (1.70,5637.50)
KIRP CALD1 0.632 0.88 (0.52,1.49) 5 0.013 0.11 (0.02,0.63) cg04874031 0.007 149.57 (3.97,5636.65)
        cg16253634 0.019 148.62 (2.24,9849.90)
        cg24956866 0.027 97.96 (1.70,5637.50)
KIRP CCL28 0.918 1.01 (0.82,1.25) 2 0.009 7.17 (1.64,31.37) cg04187185 0.365 0.50 (0.11,2.26)
        cg16324633 0.027 10.72 (1.31,87.54)
KIRP CIRBP 0.004 0.38 (0.20,0.73) 8.2:8.3 0.011 82.29 (2.75,2460.57) cg02644867 0.480 3.51 (0.11,113.99)
KIRP DNASE1L1 0.118 2.15 (0.82,5.63) 3.1 0.030 29.90 (1.40,637.29) cg21459545 0.251 0.32 (0.05,2.24)
        cg22562219 0.081 0.08 (0.01,1.36)
        cg24834461 0.224 0.20 (0.02,2.63)
KIRP PIGQ 0.703 0.88 (0.46,1.68) 3 0.047 0.05 (0.00,0.96) cg03815552 0.575 0.23 (0.00,38.74)
KIRP SLC9A3R2 0.650 1.11 (0.70,1.78) 3 0.020 0.05 (0.00,0.62) cg08601673 0.263 0.16 (0.01,3.97)
KIRP TM4SF18 0.001 0.58 (0.41,0.81) 2.1 0.015 0.04 (0.00,0.55) cg11011913 0.087 4.98 (0.79,31.30)
LIHC C1QTNF1 0.580 1.03 (0.93,1.13) 5 0.008 0.27 (0.10,0.70) cg23882796 0.553 1.24 (0.61,2.51)
LUAD GALK2 0.013 1.58 (1.10,2.26) 3.1 0.002 13.29 (2.53,69.98) cg08036668 0.219 0.42 (0.11,1.67)
LUSC AHCYL2 0.158 1.14 (0.95,1.36) 3 0.031 1.88 (1.06,3.33) cg15664152 0.933 1.03 (0.51,2.06)
LUSC AQP1 0.022 1.13 (1.02,1.26) 7.1 0.046 3.51 (1.02,12.06) cg07135629 0.952 1.04 (0.32,3.41)
        cg04551925 0.790 0.86 (0.28,2.65)
        cg10132917 0.645 1.29 (0.44,3.82)
        cg11827925 0.141 1.95 (0.80,4.73)
        cg04372674 0.049 2.22 (1.00,4.89)
        cg25075794 0.047 2.20 (1.01,4.79)
        cg25230363 0.038 2.42 (1.05,5.57)
LUSC AQP1 0.022 1.13 (1.02,1.26) 7.1 0.046 3.51 (1.02,12.06) cg26923410 0.052 2.42 (0.99,5.90)
        cg15373767 0.122 2.07 (0.82,5.21)
        cg18080604 0.049 2.74 (1.00,7.50)
        cg09676669 0.078 2.31 (0.91,5.84)
LUSC ARHGAP24 0.279 0.92 (0.80,1.07) 6 0.042 145.84 (1.20,17,748.46) cg14376467 0.908 1.04 (0.52,2.09)
        cg13889934 0.997 1.00 (0.48,2.11)
        cg21446955 0.892 1.05 (0.49,2.24)
LUSC ERG 0.738 1.03 (0.86,1.24) 5 0.038 2.25 (1.05,4.86) cg01613817 0.581 0.78 (0.32,1.91)
LUSC FAXDC2 0.285 1.07 (0.94,1.22) 5.1 0.047 2.09 (1.01,4.31) cg02379533 0.624 0.76 (0.25,2.28)
LUSC GCNT2 0.970 1.00 (0.89,1.12) 6.1 0.012 2.21 (1.19,4.11) cg13411789 0.146 0.66 (0.37,1.16)
LUSC IL1RN 0.721 0.98 (0.89,1.08) 3 0.046 0.55 (0.31,0.99) cg11783497 0.833 1.11 (0.42,2.89)
LUSC NAV1 0.569 0.96 (0.85,1.09) 6 0.024 0.49 (0.26,0.91) cg01411786 0.765 1.16 (0.44,3.03)
        cg05091570 0.982 0.99 (0.39,2.50)
        cg13877974 0.356 0.55 (0.15,1.97)
        cg16023122 0.334 0.48 (0.11,2.13)
        cg01828733 0.350 0.59 (0.19,1.79)
LUSC PLEC 0.133 1.13 (0.96,1.32) 4 0.006 23.29 (2.50,216.60) cg00329447 0.117 0.53 (0.24,1.17)
        cg06452769 0.033 0.41 (0.18,0.93)
PRAD EXOC7 0.346 0.61 (0.22,1.70) 8.2 0.038 40.29 (1.22,1329.36) cg04470878 0.660 4.86 (0.00,5523.54)
PRAD FHAD1 0.358 1.14 (0.86,1.53) 15.2 0.041 0.26 (0.07,0.95) cg07312051 0.675 5.04 (0.00,9748.17)
PRAD PCDHA9 0.592 0.94 (0.75,1.17) 1.2 0.007 14.70 (2.12,102.01) cg18029321 0.548 28.37 (0.00,1,537,765.42)
THCA EGFLAM 0.828 1.06 (0.65,1.73) 20.1 0.028 0.10 (0.01,0.78) cg21201393 0.705 1.97 (0.60,64.65)
  1. Abbreviation: KIRC Kidney renal clear cell carcinoma, KIRP Kidney renal papillary carcinoma, LUSC Lung squamous cell carcinoma, HR Hazard ratio
  2. The Cox regression model adjusted for age, gender, TNM stage, and adjuvant therapy