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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