Skip to main content

Table 1 Information on 30 mutation features

From: Discovering the molecular differences between right- and left-sided colon cancer using machine learning methods

Mutationa

avsnp150b

Gene.refGenec

weightsd

Sample Number in LCC(%)e

Sample Number in RCC_(%)f

P valueg

chr7_140753336_140753336_A_T

rs113488022

BRAF

0.12

2 (1.8)

35 (20.5)

4.72E-15

chr12_25245347_25245347_C_T

rs112445441

KRAS

0.09

5 (4.5)

20 (11.7)

4.07E-08

chr5_112839942_112839942_C_T

rs121913332

APC

0.09

1 (0.9)

18 (10.5)

2.93E-07

chr12_25245350_25245350_C_G

rs121913529

KRAS

0.09

1 (0.9)

6 (3.5)

0.02

chr12_25245350_25245350_C_T

rs121913529

KRAS

0.07

8 (7.1)

26 (15.2)

8.74E-11

chr17_7674220_7674220_C_T

rs11540652

TP53

0.06

10 (8.9)

2 (1.2)

0.56

chr7_135929761_135929762_AT_A

.

LUZP6;MTPN

0.06

4 (3.6)

2 (1.2)

0.56

chr3_179234297_179234297_A_G

rs121913279

PIK3CA

0.05

5 (4.5)

7 (4.1)

0.01

chr12_25245350_25245350_C_A

rs121913529

KRAS

0.04

11 (9.8)

13 (7.6)

3.46E-05

chr3_179218294_179218294_G_A

rs121913273

PIK3CA

0.04

4 (3.6)

5 (2.9)

0.04

chr12_25225628_25225628_C_T

rs121913527

KRAS

0.03

2 (1.8)

6 (3.5)

0.02

chr5_112780895_112780895_C_T

rs587781392

APC

0.03

4 (3.6)

4 (2.3)

0.08

chr5_78039082_78039083_GT_G

.

AP3B1

0.03

2 (1.8)

10 (5.8)

5.37E-4

chr15_23567535_23567536_CT_C

.

MKRN3

0.02

1 (0.9)

15 (8.8)

5.29E-06

chr17_7673802_7673802_C_T

rs28934576

TP53

0.02

5 (4.5)

6 (3.5)

0.02

chr3_46375665_46375666_TG_T

rs939905165

LOC102724297

0.02

0 (0)

15 (8.8)

5.29E-06

chr1_244056271_244056272_GA_G

rs972665297

ZBTB18

0.02

2 (1.8)

17 (9.9)

7.77E-07

chr7_1747914_1747915_TA_T

.

ELFN1

0.02

2 (1.8)

8 (4.7)

3.08E-3

chr12_109581434_109581435_GC_G

.

MVK

0.02

0 (0)

11 (6.4)

2.16E-4

chr4_105242265_105242266_CT_C

.

TET2-AS1

0.02

1 (0.9)

8 (4.7)

3.08E-3

chr8_13568071_13568072_CT_C

rs1014242184

C8orf48

0.01

1 (0.9)

14 (8.2)

1.36E-05

chr17_58357799_58357800_AC_A

rs781215815

RNF43

0.01

0 (0)

17 (9.9)

7.77E-07

chr2_68464196_68464197_AT_A

.

FBXO48

0.01

0 (0)

9 (5.3)

1.29E-3

chr4_154609909_154609910_GT_G

.

FGG

0.01

0 (0)

10 (5.8)

5.32E-4

chr17_7675088_7675088_C_T

rs28934578

TP53

0.01

10 (8.9)

13 (7.6)

3.46E-05

chr2_147926116_147926117_TA_T

rs764719749

ACVR2A

0.01

1 (0.9)

11 (6.4)

2.16E-4

chr5_112838220_112838220_C_T

rs121913333

APC

0.01

3 (2.7)

7 (4.1)

7.22E-3

chr13_108232109_108232110_CA_C

rs977361714

ABHD13

0.003

1 (0.9)

9 (5.3)

1.29E-3

chr4_44698597_44698598_GA_G

.

GUF1

0.003

1 (0.9)

11 (6.4)

2.16E-4

chr6_98837428_98837429_CT_C

rs898072886

POU3F2

0.003

1 (0.9)

10 (5.8)

5.32E-4

  1. aPosition of variants. For example, chr7_140753336_140753336_A_T represents base A being replaced by T at position 140,753,336 of chromosome 7
  2. bThe annotation of variants with dbSNP identifiers by ANNOVAR
  3. cThe annotated genes of the variants by ANNOVAR
  4. dThe weights (importance) of the mutation features for the classification model
  5. eThe number of samples (percent of samples) with the variants among LCC samples
  6. fThe number of samples (percent of samples) with the variants among RCC samples
  7. gThe P-value from Fisher’s exact test for each variant