Copy Number
The putative cancer-associated PDGs driven by SCNAs in each cancer type were identified by four criteria: 1) located in a peak region of a significantly recurrent focal SNCA locus estimated by the genomic identification of significant targets in cancer (GISTIC2) algorithm, (q≤0.25); 2) altered with high frequency and large amplitude (G-score ≥0.1); 3) mRNA reliably detected in at least 10% of tumor specimens in the given cancer type (90th percentile of FPKM value ≥1); and 4) mRNA significantly and positively correlated with copy numbers (Pearson P-value less than 0.001).
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| KIRC | KIRP | KICH | PRAD | BLCA | THYM | MESO | LUAD | LUSC | HNSC | ESCA | STAD | COAD | READ | PAAD | LIHC | CHOL | ACC | PCPG | THCA | BRCA | OV | CESC | UCEC | UCS | SARC | TGCT | LAML | DLBC | LGG | GBM | UVM | SKCM | |||||||||||||||||||||||||||||||||||
| HGNC Symbol | Ensembl Gene ID | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del |
| COL4A1 | ENSG00000187498 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.04 | 0.02 | 0.23 | 0.02 | 0.00 | 0.01 | 0.03 | 0.00 | 0.12 | 0.04 | 0.16 | 0.05 | 0.14 | 0.02 | 0.16 | 0.04 | 0.16 | 0.04 | 0.13 | 0.01 | 0.16 | 0.01 | 0.02 | 0.02 | 0.29 | 0.00 | 0.17 | 0.04 | 0.03 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.16 | 0.04 | 0.26 | 0.09 | 0.23 | 0.02 | 0.10 | 0.02 | 0.42 | 0.06 | 0.30 | 0.15 | 0.01 | 0.01 | 0.00 | 0.00 | 0.02 | 0.12 | 0.06 | 0.02 | 0.07 | 0.03 | 0.05 | 0.00 | 0.06 | 0.07 |
| CD244 | ENSG00000122223 | 0.03 | 0.00 | 0.02 | 0.01 | 0.00 | 0.03 | 0.02 | 0.05 | 0.90 | 0.00 | 0.02 | 0.00 | 0.10 | 0.02 | 0.27 | 0.00 | 0.29 | 0.00 | 0.06 | 0.00 | 0.29 | 0.00 | 0.14 | 0.00 | 0.03 | 0.00 | 0.12 | 0.00 | 0.06 | 0.00 | 0.30 | 0.00 | 0.30 | 0.01 | 0.16 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.33 | 0.00 | 0.37 | 0.02 | 0.18 | 0.00 | 0.14 | 0.00 | 0.41 | 0.00 | 0.47 | 0.02 | 0.10 | 0.00 | 0.00 | 0.00 | 0.25 | 0.00 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.17 | 0.01 |
| GHR | ENSG00000112964 | 0.00 | 0.00 | 0.00 | 0.01 | 0.03 | 0.00 | 0.01 | 0.02 | 0.13 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.18 | 0.01 | 0.24 | 0.01 | 0.10 | 0.01 | 0.17 | 0.01 | 0.20 | 0.01 | 0.05 | 0.01 | 0.05 | 0.00 | 0.04 | 0.00 | 0.05 | 0.00 | 0.00 | 0.01 | 0.11 | 0.02 | 0.01 | 0.02 | 0.00 | 0.00 | 0.09 | 0.02 | 0.22 | 0.02 | 0.07 | 0.00 | 0.08 | 0.01 | 0.25 | 0.03 | 0.25 | 0.02 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.00 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.14 | 0.03 |
| ALOX5AP | ENSG00000132965 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.09 | 0.15 | 0.05 | 0.00 | 0.02 | 0.00 | 0.18 | 0.02 | 0.08 | 0.04 | 0.11 | 0.02 | 0.14 | 0.12 | 0.06 | 0.15 | 0.03 | 0.16 | 0.00 | 0.27 | 0.02 | 0.01 | 0.01 | 0.02 | 0.15 | 0.00 | 0.14 | 0.00 | 0.09 | 0.00 | 0.00 | 0.00 | 0.01 | 0.12 | 0.07 | 0.06 | 0.18 | 0.02 | 0.16 | 0.01 | 0.05 | 0.01 | 0.15 | 0.10 | 0.28 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.11 | 0.02 | 0.05 | 0.01 | 0.07 | 0.00 | 0.00 | 0.08 | 0.02 |
| PLA2R1 | ENSG00000153246 | 0.02 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.10 | 0.11 | 0.03 | 0.00 | 0.01 | 0.00 | 0.00 | 0.05 | 0.01 | 0.10 | 0.03 | 0.05 | 0.02 | 0.12 | 0.03 | 0.03 | 0.05 | 0.01 | 0.02 | 0.01 | 0.02 | 0.05 | 0.01 | 0.05 | 0.07 | 0.00 | 0.05 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.03 | 0.33 | 0.04 | 0.05 | 0.01 | 0.08 | 0.01 | 0.06 | 0.00 | 0.06 | 0.10 | 0.03 | 0.01 | 0.00 | 0.00 | 0.00 | 0.15 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.01 |
| TDRKH | ENSG00000182134 | 0.03 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.07 | 0.00 | 0.59 | 0.01 | 0.02 | 0.00 | 0.11 | 0.02 | 0.41 | 0.00 | 0.30 | 0.00 | 0.06 | 0.01 | 0.30 | 0.00 | 0.22 | 0.00 | 0.02 | 0.00 | 0.17 | 0.00 | 0.07 | 0.00 | 0.36 | 0.00 | 0.43 | 0.01 | 0.20 | 0.00 | 0.10 | 0.00 | 0.00 | 0.00 | 0.35 | 0.00 | 0.65 | 0.02 | 0.22 | 0.00 | 0.30 | 0.00 | 0.68 | 0.00 | 0.47 | 0.03 | 0.12 | 0.01 | 0.00 | 0.00 | 0.24 | 0.04 | 0.01 | 0.00 | 0.05 | 0.00 | 0.00 | 0.00 | 0.21 | 0.00 |
| SV2B | ENSG00000185518 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.02 | 0.01 | 0.04 | 0.03 | 0.03 | 0.00 | 0.06 | 0.00 | 0.05 | 0.01 | 0.20 | 0.00 | 0.06 | 0.02 | 0.23 | 0.01 | 0.24 | 0.01 | 0.05 | 0.01 | 0.10 | 0.00 | 0.06 | 0.00 | 0.06 | 0.05 | 0.05 | 0.01 | 0.09 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.16 | 0.02 | 0.34 | 0.08 | 0.18 | 0.01 | 0.05 | 0.02 | 0.32 | 0.05 | 0.14 | 0.03 | 0.00 | 0.01 | 0.00 | 0.00 | 0.06 | 0.00 | 0.02 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.19 | 0.01 |
| MUC4 | ENSG00000145113 | 0.05 | 0.01 | 0.03 | 0.01 | 0.00 | 0.01 | 0.03 | 0.06 | 0.19 | 0.01 | 0.00 | 0.00 | 0.00 | 0.07 | 0.14 | 0.06 | 1.38 | 0.01 | 0.57 | 0.00 | 0.82 | 0.04 | 0.23 | 0.02 | 0.06 | 0.01 | 0.06 | 0.02 | 0.03 | 0.01 | 0.12 | 0.03 | 0.12 | 0.03 | 0.10 | 0.03 | 0.00 | 0.10 | 0.00 | 0.00 | 0.22 | 0.03 | 1.02 | 0.09 | 0.65 | 0.00 | 0.37 | 0.01 | 0.79 | 0.15 | 0.09 | 0.14 | 0.14 | 0.03 | 0.01 | 0.00 | 0.35 | 0.04 | 0.03 | 0.07 | 0.06 | 0.09 | 0.00 | 0.00 | 0.03 | 0.03 |
| HCN2 | ENSG00000099822 | 0.00 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.02 | 0.02 | 0.14 | 0.05 | 0.00 | 0.03 | 0.09 | 0.03 | 0.09 | 0.03 | 0.15 | 0.01 | 0.15 | 0.05 | 0.18 | 0.03 | 0.07 | 0.01 | 0.06 | 0.02 | 0.09 | 0.01 | 0.07 | 0.03 | 0.13 | 0.04 | 0.03 | 0.12 | 0.01 | 0.03 | 0.01 | 0.00 | 0.01 | 0.02 | 0.17 | 0.03 | 0.92 | 0.05 | 0.23 | 0.03 | 0.25 | 0.00 | 0.84 | 0.23 | 0.22 | 0.01 | 0.01 | 0.00 | 0.01 | 0.03 | 0.00 | 0.06 | 0.02 | 0.08 | 0.01 | 0.01 | 0.03 | 0.02 | 0.08 |
| SLC5A1 | ENSG00000100170 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.02 | 0.00 | 0.03 | 0.18 | 0.01 | 0.02 | 0.03 | 0.00 | 0.01 | 0.04 | 0.02 | 0.12 | 0.02 | 0.02 | 0.00 | 0.06 | 0.01 | 0.02 | 0.02 | 0.02 | 0.01 | 0.02 | 0.01 | 0.01 | 0.02 | 0.02 | 0.01 | 0.00 | 0.01 | 0.00 | 0.02 | 0.00 | 0.02 | 0.00 | 0.00 | 0.04 | 0.03 | 0.19 | 0.07 | 0.04 | 0.00 | 0.10 | 0.02 | 0.20 | 0.11 | 0.08 | 0.03 | 0.05 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.01 | 0.05 | 0.00 | 0.00 | 0.05 | 0.04 |
| CACNG4 | ENSG00000075461 | 0.02 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.23 | 0.01 | 0.02 | 0.00 | 0.12 | 0.00 | 0.17 | 0.00 | 0.19 | 0.00 | 0.07 | 0.02 | 0.19 | 0.04 | 0.11 | 0.03 | 0.09 | 0.01 | 0.10 | 0.01 | 0.05 | 0.10 | 0.20 | 0.00 | 0.12 | 0.01 | 0.15 | 0.09 | 0.02 | 0.01 | 0.00 | 0.00 | 0.55 | 0.01 | 0.26 | 0.03 | 0.15 | 0.03 | 0.11 | 0.02 | 0.45 | 0.02 | 0.22 | 0.04 | 0.02 | 0.00 | 0.00 | 0.00 | 0.05 | 0.07 | 0.06 | 0.00 | 0.02 | 0.00 | 0.17 | 0.01 | 0.24 | 0.01 |
| NPM1 | ENSG00000181163 | 0.33 | 0.00 | 0.05 | 0.01 | 0.00 | 0.00 | 0.04 | 0.00 | 0.01 | 0.10 | 0.00 | 0.00 | 0.02 | 0.06 | 0.11 | 0.04 | 0.02 | 0.05 | 0.02 | 0.06 | 0.07 | 0.03 | 0.03 | 0.04 | 0.01 | 0.01 | 0.04 | 0.04 | 0.02 | 0.02 | 0.12 | 0.03 | 0.05 | 0.01 | 0.30 | 0.02 | 0.00 | 0.03 | 0.01 | 0.00 | 0.08 | 0.03 | 0.21 | 0.12 | 0.03 | 0.02 | 0.04 | 0.02 | 0.16 | 0.01 | 0.16 | 0.07 | 0.00 | 0.00 | 0.00 | 0.02 | 0.02 | 0.00 | 0.01 | 0.07 | 0.02 | 0.04 | 0.04 | 0.00 | 0.04 | 0.09 |
| WNK3 | ENSG00000196632 | 0.01 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.03 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.02 | 0.08 | 0.03 | 0.04 | 0.03 | 0.05 | 0.03 | 0.03 | 0.01 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.13 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.09 | 0.01 | 0.23 | 0.04 | 0.02 | 0.03 | 0.06 | 0.02 | 0.31 | 0.03 | 0.21 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.07 | 0.00 | 0.08 | 0.00 | 0.03 | 0.00 | 0.03 | 0.00 | 0.02 | 0.00 |
| SSH2 | ENSG00000141298 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.01 | 0.26 | 0.01 | 0.05 | 0.00 | 0.00 | 0.05 | 0.07 | 0.01 | 0.06 | 0.05 | 0.02 | 0.03 | 0.13 | 0.04 | 0.12 | 0.01 | 0.08 | 0.01 | 0.08 | 0.01 | 0.04 | 0.02 | 0.04 | 0.00 | 0.09 | 0.02 | 0.04 | 0.05 | 0.00 | 0.18 | 0.00 | 0.00 | 0.31 | 0.06 | 0.09 | 0.13 | 0.04 | 0.03 | 0.12 | 0.05 | 0.14 | 0.08 | 0.04 | 0.20 | 0.00 | 0.02 | 0.00 | 0.03 | 0.04 | 0.00 | 0.00 | 0.02 | 0.01 | 0.04 | 0.00 | 0.03 | 0.03 | 0.04 |
| PCSK2 | ENSG00000125851 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.02 | 0.05 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.04 | 0.03 | 0.08 | 0.01 | 0.04 | 0.02 | 0.04 | 0.02 | 0.03 | 0.02 | 0.06 | 0.04 | 0.12 | 0.04 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.01 | 0.01 | 0.07 | 0.01 | 0.00 | 0.00 | 0.00 | 0.06 | 0.03 | 0.13 | 0.06 | 0.03 | 0.02 | 0.04 | 0.01 | 0.09 | 0.02 | 0.07 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.02 |
| ABCB9 | ENSG00000150967 | 0.01 | 0.01 | 0.02 | 0.00 | 0.07 | 0.02 | 0.03 | 0.04 | 0.09 | 0.03 | 0.00 | 0.00 | 0.01 | 0.02 | 0.03 | 0.05 | 0.02 | 0.07 | 0.03 | 0.03 | 0.09 | 0.05 | 0.05 | 0.05 | 0.01 | 0.01 | 0.05 | 0.03 | 0.00 | 0.06 | 0.04 | 0.09 | 0.00 | 0.17 | 0.10 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.05 | 0.09 | 0.14 | 0.24 | 0.03 | 0.02 | 0.06 | 0.07 | 0.26 | 0.16 | 0.15 | 0.06 | 0.01 | 0.00 | 0.00 | 0.01 | 0.07 | 0.06 | 0.04 | 0.01 | 0.02 | 0.01 | 0.00 | 0.00 | 0.04 | 0.07 |
| NETO2 | ENSG00000171208 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.07 | 0.01 | 0.07 | 0.02 | 0.01 | 0.00 | 0.00 | 0.04 | 0.07 | 0.04 | 0.05 | 0.03 | 0.05 | 0.04 | 0.11 | 0.02 | 0.02 | 0.03 | 0.04 | 0.01 | 0.02 | 0.01 | 0.01 | 0.01 | 0.07 | 0.01 | 0.00 | 0.08 | 0.08 | 0.04 | 0.00 | 0.01 | 0.00 | 0.00 | 0.08 | 0.05 | 0.12 | 0.14 | 0.02 | 0.07 | 0.03 | 0.05 | 0.09 | 0.14 | 0.06 | 0.15 | 0.08 | 0.01 | 0.02 | 0.00 | 0.00 | 0.04 | 0.00 | 0.00 | 0.01 | 0.02 | 0.00 | 0.03 | 0.01 | 0.06 |
| ABCC9 | ENSG00000069431 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.02 | 0.06 | 0.08 | 0.04 | 0.01 | 0.00 | 0.00 | 0.02 | 0.21 | 0.04 | 0.17 | 0.01 | 0.06 | 0.01 | 0.15 | 0.01 | 0.14 | 0.03 | 0.01 | 0.01 | 0.05 | 0.03 | 0.07 | 0.04 | 0.01 | 0.03 | 0.14 | 0.07 | 0.06 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.09 | 0.04 | 0.35 | 0.06 | 0.02 | 0.01 | 0.05 | 0.01 | 0.17 | 0.03 | 0.21 | 0.08 | 0.62 | 0.00 | 0.00 | 0.01 | 0.00 | 0.04 | 0.08 | 0.01 | 0.04 | 0.02 | 0.00 | 0.00 | 0.05 | 0.01 |
| CACNA1C | ENSG00000151067 | 0.02 | 0.00 | 0.01 | 0.01 | 0.02 | 0.00 | 0.02 | 0.06 | 0.13 | 0.03 | 0.01 | 0.00 | 0.04 | 0.01 | 0.10 | 0.07 | 0.22 | 0.01 | 0.16 | 0.01 | 0.17 | 0.03 | 0.13 | 0.07 | 0.16 | 0.01 | 0.17 | 0.03 | 0.13 | 0.04 | 0.04 | 0.04 | 0.26 | 0.05 | 0.05 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.16 | 0.04 | 0.45 | 0.09 | 0.05 | 0.03 | 0.10 | 0.02 | 0.22 | 0.16 | 0.20 | 0.13 | 0.57 | 0.00 | 0.00 | 0.01 | 0.02 | 0.03 | 0.15 | 0.01 | 0.07 | 0.02 | 0.00 | 0.01 | 0.06 | 0.02 |
| DCLK1 | ENSG00000133083 | 0.02 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.22 | 0.08 | 0.13 | 0.00 | 0.02 | 0.00 | 0.18 | 0.02 | 0.08 | 0.02 | 0.10 | 0.01 | 0.16 | 0.07 | 0.09 | 0.15 | 0.03 | 0.12 | 0.02 | 0.18 | 0.02 | 0.01 | 0.01 | 0.00 | 0.18 | 0.00 | 0.14 | 0.00 | 0.03 | 0.01 | 0.00 | 0.00 | 0.01 | 0.07 | 0.12 | 0.06 | 0.19 | 0.02 | 0.19 | 0.02 | 0.05 | 0.07 | 0.23 | 0.10 | 0.27 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.06 | 0.00 | 0.06 | 0.02 | 0.10 | 0.00 | 0.00 | 0.06 | 0.03 |
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