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Table 3 Top 25 candidates associated with advanced clinical stage

From: Systematic genomic identification of colorectal cancer genes delineating advanced from early clinical stage and metastasis

 

Gene

 

Elastic-net Feature Rank

Gene

Chr

Score

Copy Number

Gene Expression

Methylation

Mutation

WRN*

8p12

27.03

5 ↓

106 ↓

29 ↑

 

SYK*

9q22.2

24.09

 

13 ↓

6 ↓

 

DDX5*

17q23.3

18.94

70 ↓

12 ↓

  

ADRA2C

4p16.3

18.13

 

11 ↑

81 ↓

 

GNAS*

20q13.32

16.9

  

39 ↓

68 ↑

SEMA3B

3p21.31

16.66

 

82 ↓

28 ↓

 

HSD17B2

16q23.3

14.45

17 ↑

120 ↑

  

TTN

2q31.2

13.72

 

80 ↓

 

66 ↓

FHIT*

3p14.2

13.56

  

71 ↑

77 ↓

HIST1H4I*

6p22.1

12.82

 

35 ↑

122 ↓

 

FOXP4

6p21.1

12.74

  

1 ↓

 

REEP5

5q22.2

12.66

 

2 ↑

  

PDK4

7q21.3

12.58

 

3 ↑

  

OR51E2

11p15.4

12.49

 

4 ↑

  

S100P

4p16.1

12.25

 

7 ↓

  

HIP1*

7q11.23

12.17

 

8 ↑

  

ZNF570

19q13.12

12.09

 

50 ↑

 

116 ↓

SDHC*

1q23.3

12.09

 

9 ↑

  

DDIT3*

12q13.3

12

 

10 ↑

  

CRTC1*

19p13.11

11.92

  

130 ↑

38 ↓

FCRL4*

1q23.1

11.84

 

14 ↓

155 ↓

 

SLC22A11

11q13.1

11.6

 

15 ↓

  

FLT1

13q12.2

11.51

 

16 ↑

  

CYP26B1

2p13.2

11.35

 

18 ↓

  

RNF113A

Xq24

11.27

  

19 ↑

 
  1. We ranked the genes by selected feature scoring (see Method for scoring scheme). This scoring scheme selects genes that are supported by multiple and/or highly ranked genomic features. Elastic-net feature rank indicates the rank of individual assay features, where ↑ indicates a direct association with the feature value and ↓ indicates inverse association with the feature value. COSMIC-annotated cancer genes are marked by *.
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BMC Medical Genomics

ISSN: 1755-8794

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