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 *.

Lee et al.

Lee et al. BMC Medical Genomics 2013 6:54   doi:10.1186/1755-8794-6-54

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