Table 3.
Top 25 candidates associated with advanced clinical stage
| 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 ↑ | |||
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 *.