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 |
| CHEK1 | ENSG00000149554 | 0.00 | 0.01 | 0.00 | 0.05 | 0.00 | 0.02 | 0.02 | 0.06 | 0.03 | 0.11 | 0.00 | 0.00 | 0.11 | 0.04 | 0.05 | 0.09 | 0.04 | 0.10 | 0.04 | 0.14 | 0.05 | 0.14 | 0.05 | 0.08 | 0.01 | 0.01 | 0.01 | 0.03 | 0.01 | 0.02 | 0.02 | 0.09 | 0.00 | 0.19 | 0.00 | 0.06 | 0.00 | 0.05 | 0.00 | 0.00 | 0.04 | 0.22 | 0.21 | 0.17 | 0.04 | 0.32 | 0.04 | 0.08 | 0.05 | 0.17 | 0.02 | 0.25 | 0.00 | 0.28 | 0.04 | 0.00 | 0.13 | 0.02 | 0.06 | 0.01 | 0.01 | 0.01 | 0.00 | 0.07 | 0.00 | 0.26 |
| KLF5 | ENSG00000102554 | 0.01 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.27 | 0.21 | 0.11 | 0.00 | 0.02 | 0.00 | 0.06 | 0.09 | 0.05 | 0.11 | 0.07 | 0.24 | 0.04 | 0.22 | 0.06 | 0.25 | 0.03 | 0.19 | 0.01 | 0.28 | 0.01 | 0.02 | 0.01 | 0.07 | 0.14 | 0.00 | 0.17 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.04 | 0.08 | 0.13 | 0.11 | 0.17 | 0.06 | 0.04 | 0.03 | 0.29 | 0.11 | 0.13 | 0.22 | 0.00 | 0.02 | 0.00 | 0.00 | 0.04 | 0.06 | 0.00 | 0.08 | 0.01 | 0.12 | 0.05 | 0.00 | 0.04 | 0.02 |
| AURKB | ENSG00000178999 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.15 | 0.03 | 0.02 | 0.00 | 0.01 | 0.00 | 0.03 | 0.01 | 0.05 | 0.01 | 0.02 | 0.02 | 0.03 | 0.03 | 0.04 | 0.01 | 0.02 | 0.00 | 0.01 | 0.00 | 0.02 | 0.01 | 0.02 | 0.00 | 0.16 | 0.01 | 0.03 | 0.01 | 0.05 | 0.00 | 0.03 | 0.00 | 0.00 | 0.01 | 0.06 | 0.07 | 0.07 | 0.00 | 0.04 | 0.04 | 0.05 | 0.06 | 0.15 | 0.25 | 0.26 | 0.00 | 0.02 | 0.02 | 0.01 | 0.00 | 0.10 | 0.01 | 0.00 | 0.00 | 0.06 | 0.00 | 0.00 | 0.00 | 0.04 |
| TYMS | ENSG00000176890 | 0.00 | 0.00 | 0.01 | 0.00 | 0.01 | 0.01 | 0.01 | 0.03 | 0.08 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.02 | 0.18 | 0.04 | 0.18 | 0.03 | 0.30 | 0.06 | 0.07 | 0.02 | 0.02 | 0.01 | 0.02 | 0.05 | 0.03 | 0.03 | 0.02 | 0.02 | 0.00 | 0.05 | 0.00 | 0.06 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.04 | 0.15 | 0.11 | 0.06 | 0.03 | 0.06 | 0.03 | 0.10 | 0.07 | 0.12 | 0.12 | 0.00 | 0.11 | 0.00 | 0.01 | 0.03 | 0.04 | 0.02 | 0.03 | 0.01 | 0.04 | 0.00 | 0.00 | 0.05 | 0.02 |
| AURKA | ENSG00000087586 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.01 | 0.06 | 0.03 | 0.00 | 0.00 | 0.03 | 0.00 | 0.17 | 0.02 | 0.04 | 0.03 | 0.01 | 0.01 | 0.11 | 0.01 | 0.18 | 0.00 | 0.13 | 0.00 | 0.12 | 0.00 | 0.02 | 0.01 | 0.09 | 0.01 | 0.00 | 0.01 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.33 | 0.01 | 0.35 | 0.04 | 0.03 | 0.02 | 0.09 | 0.01 | 0.16 | 0.00 | 0.17 | 0.04 | 0.03 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.10 | 0.00 |
| ESR1 | ENSG00000091831 | 0.00 | 0.06 | 0.00 | 0.01 | 0.00 | 0.05 | 0.01 | 0.02 | 0.03 | 0.08 | 0.00 | 0.02 | 0.00 | 0.17 | 0.03 | 0.06 | 0.07 | 0.05 | 0.03 | 0.03 | 0.10 | 0.04 | 0.09 | 0.04 | 0.02 | 0.01 | 0.04 | 0.01 | 0.00 | 0.04 | 0.01 | 0.12 | 0.00 | 0.16 | 0.15 | 0.06 | 0.00 | 0.02 | 0.00 | 0.00 | 0.14 | 0.08 | 0.14 | 0.39 | 0.01 | 0.09 | 0.15 | 0.05 | 0.43 | 0.08 | 0.29 | 0.02 | 0.01 | 0.04 | 0.00 | 0.00 | 0.00 | 0.07 | 0.00 | 0.05 | 0.01 | 0.09 | 0.05 | 0.09 | 0.02 | 0.14 |
| ERG | ENSG00000157554 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.30 | 0.05 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.02 | 0.03 | 0.06 | 0.02 | 0.04 | 0.04 | 0.09 | 0.03 | 0.07 | 0.01 | 0.02 | 0.01 | 0.08 | 0.01 | 0.01 | 0.01 | 0.01 | 0.07 | 0.03 | 0.00 | 0.04 | 0.01 | 0.00 | 0.00 | 0.00 | 0.08 | 0.02 | 0.14 | 0.11 | 0.10 | 0.02 | 0.04 | 0.01 | 0.04 | 0.03 | 0.09 | 0.07 | 0.04 | 0.00 | 0.17 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.02 | 0.03 | 0.00 | 0.01 | 0.01 |
| CDK1 | ENSG00000170312 | 0.00 | 0.01 | 0.00 | 0.01 | 0.03 | 0.00 | 0.03 | 0.04 | 0.03 | 0.04 | 0.00 | 0.00 | 0.01 | 0.04 | 0.06 | 0.02 | 0.07 | 0.04 | 0.06 | 0.02 | 0.08 | 0.07 | 0.09 | 0.02 | 0.01 | 0.03 | 0.00 | 0.02 | 0.01 | 0.00 | 0.03 | 0.02 | 0.31 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.14 | 0.03 | 0.13 | 0.11 | 0.02 | 0.01 | 0.09 | 0.03 | 0.56 | 0.03 | 0.03 | 0.08 | 0.00 | 0.01 | 0.00 | 0.00 | 0.03 | 0.00 | 0.01 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.04 |
| JAK2 | ENSG00000096968 | 0.02 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.05 | 0.17 | 0.13 | 0.01 | 0.01 | 0.04 | 0.07 | 0.06 | 0.11 | 0.15 | 0.11 | 0.25 | 0.06 | 0.15 | 0.13 | 0.17 | 0.10 | 0.01 | 0.03 | 0.06 | 0.04 | 0.01 | 0.08 | 0.07 | 0.03 | 0.03 | 0.01 | 0.12 | 0.03 | 0.01 | 0.03 | 0.00 | 0.00 | 0.10 | 0.06 | 0.21 | 0.20 | 0.24 | 0.04 | 0.08 | 0.02 | 0.02 | 0.12 | 0.22 | 0.10 | 0.01 | 0.10 | 0.00 | 0.00 | 0.07 | 0.05 | 0.00 | 0.09 | 0.01 | 0.18 | 0.00 | 0.00 | 0.09 | 0.11 |
| KIT | ENSG00000157404 | 0.01 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.01 | 0.02 | 0.12 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.12 | 0.01 | 0.44 | 0.01 | 0.08 | 0.01 | 0.14 | 0.05 | 0.04 | 0.03 | 0.03 | 0.01 | 0.02 | 0.03 | 0.02 | 0.02 | 0.02 | 0.05 | 0.00 | 0.08 | 0.03 | 0.00 | 0.02 | 0.02 | 0.00 | 0.00 | 0.08 | 0.01 | 0.20 | 0.04 | 0.08 | 0.02 | 0.05 | 0.00 | 0.20 | 0.05 | 0.23 | 0.03 | 0.37 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.15 | 0.00 | 0.68 | 0.01 | 0.00 | 0.02 | 0.13 | 0.02 |
| PIK3CA | ENSG00000121879 | 0.07 | 0.00 | 0.03 | 0.00 | 0.00 | 0.01 | 0.08 | 0.01 | 0.20 | 0.01 | 0.00 | 0.00 | 0.00 | 0.08 | 0.15 | 0.03 | 1.85 | 0.00 | 0.71 | 0.00 | 0.79 | 0.01 | 0.26 | 0.00 | 0.04 | 0.01 | 0.06 | 0.01 | 0.04 | 0.00 | 0.13 | 0.02 | 0.12 | 0.01 | 0.10 | 0.00 | 0.00 | 0.08 | 0.00 | 0.00 | 0.27 | 0.01 | 1.22 | 0.02 | 0.72 | 0.00 | 0.40 | 0.01 | 1.10 | 0.07 | 0.09 | 0.10 | 0.19 | 0.00 | 0.00 | 0.00 | 0.06 | 0.00 | 0.07 | 0.00 | 0.18 | 0.01 | 0.00 | 0.00 | 0.04 | 0.04 |
| FGFR4 | ENSG00000160867 | 0.34 | 0.01 | 0.05 | 0.01 | 0.00 | 0.00 | 0.04 | 0.00 | 0.02 | 0.11 | 0.00 | 0.01 | 0.03 | 0.05 | 0.10 | 0.03 | 0.05 | 0.06 | 0.02 | 0.05 | 0.12 | 0.01 | 0.04 | 0.04 | 0.03 | 0.02 | 0.04 | 0.03 | 0.03 | 0.02 | 0.14 | 0.02 | 0.05 | 0.01 | 0.46 | 0.02 | 0.01 | 0.03 | 0.01 | 0.00 | 0.11 | 0.03 | 0.27 | 0.11 | 0.03 | 0.05 | 0.08 | 0.01 | 0.24 | 0.01 | 0.15 | 0.08 | 0.00 | 0.01 | 0.00 | 0.02 | 0.02 | 0.00 | 0.01 | 0.06 | 0.03 | 0.04 | 0.04 | 0.00 | 0.09 | 0.09 |
| KIF11 | ENSG00000138160 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.15 | 0.03 | 0.10 | 0.00 | 0.02 | 0.01 | 0.13 | 0.01 | 0.03 | 0.04 | 0.07 | 0.01 | 0.06 | 0.02 | 0.08 | 0.00 | 0.10 | 0.00 | 0.10 | 0.00 | 0.07 | 0.01 | 0.02 | 0.01 | 0.07 | 0.16 | 0.07 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.01 | 0.01 | 0.08 | 0.06 | 0.33 | 0.01 | 0.07 | 0.03 | 0.10 | 0.03 | 0.13 | 0.01 | 0.06 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.07 | 0.00 | 0.03 | 0.00 | 0.04 | 0.00 | 0.00 | 0.01 | 0.03 |
| TP63 | ENSG00000073282 | 0.05 | 0.00 | 0.03 | 0.01 | 0.00 | 0.01 | 0.03 | 0.04 | 0.18 | 0.01 | 0.00 | 0.00 | 0.00 | 0.07 | 0.15 | 0.05 | 1.52 | 0.00 | 0.67 | 0.00 | 0.84 | 0.02 | 0.23 | 0.01 | 0.05 | 0.02 | 0.06 | 0.02 | 0.03 | 0.00 | 0.11 | 0.03 | 0.12 | 0.03 | 0.10 | 0.00 | 0.00 | 0.10 | 0.00 | 0.00 | 0.20 | 0.02 | 0.95 | 0.08 | 0.71 | 0.00 | 0.34 | 0.02 | 0.84 | 0.09 | 0.13 | 0.09 | 0.23 | 0.00 | 0.00 | 0.00 | 0.07 | 0.01 | 0.02 | 0.04 | 0.07 | 0.07 | 0.00 | 0.00 | 0.03 | 0.04 |
| CCND1 | ENSG00000110092 | 0.01 | 0.00 | 0.03 | 0.01 | 0.09 | 0.00 | 0.10 | 0.00 | 0.86 | 0.01 | 0.00 | 0.00 | 0.08 | 0.00 | 0.23 | 0.00 | 1.10 | 0.01 | 1.90 | 0.01 | 2.79 | 0.00 | 0.44 | 0.02 | 0.02 | 0.01 | 0.07 | 0.02 | 0.04 | 0.01 | 0.55 | 0.01 | 0.76 | 0.02 | 0.06 | 0.01 | 0.02 | 0.00 | 0.00 | 0.00 | 1.31 | 0.02 | 0.43 | 0.04 | 0.28 | 0.01 | 0.16 | 0.02 | 0.19 | 0.11 | 0.21 | 0.05 | 0.00 | 0.05 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.01 | 0.01 | 0.03 | 0.00 | 0.00 | 0.44 | 0.01 |
| MITF | ENSG00000187098 | 0.00 | 0.03 | 0.00 | 0.01 | 0.00 | 0.02 | 0.00 | 0.08 | 0.04 | 0.17 | 0.00 | 0.06 | 0.01 | 0.11 | 0.03 | 0.04 | 0.00 | 0.16 | 0.03 | 0.08 | 0.02 | 0.16 | 0.07 | 0.05 | 0.02 | 0.02 | 0.03 | 0.04 | 0.06 | 0.02 | 0.02 | 0.07 | 0.00 | 0.20 | 0.08 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.15 | 0.11 | 0.13 | 0.03 | 0.14 | 0.03 | 0.07 | 0.32 | 0.26 | 0.04 | 0.09 | 0.11 | 0.01 | 0.00 | 0.03 | 0.02 | 0.00 | 0.00 | 0.03 | 0.00 | 0.03 | 0.00 | 0.00 | 0.37 | 0.01 |
| PLK1 | ENSG00000166851 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.14 | 0.03 | 0.00 | 0.00 | 0.02 | 0.04 | 0.04 | 0.01 | 0.04 | 0.01 | 0.03 | 0.02 | 0.02 | 0.01 | 0.02 | 0.01 | 0.02 | 0.01 | 0.01 | 0.00 | 0.01 | 0.00 | 0.04 | 0.01 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.04 | 0.01 | 0.07 | 0.05 | 0.01 | 0.01 | 0.03 | 0.01 | 0.17 | 0.03 | 0.01 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.09 | 0.02 | 0.00 | 0.02 | 0.00 | 0.07 | 0.00 | 0.00 | 0.01 | 0.03 |
| EEF2 | ENSG00000167658 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.04 | 0.01 | 0.03 | 0.02 | 0.13 | 0.02 | 0.00 | 0.01 | 0.10 | 0.01 | 0.08 | 0.02 | 0.12 | 0.03 | 0.11 | 0.05 | 0.11 | 0.00 | 0.10 | 0.01 | 0.04 | 0.01 | 0.10 | 0.00 | 0.06 | 0.03 | 0.14 | 0.00 | 0.03 | 0.04 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.04 | 0.11 | 0.03 | 0.87 | 0.04 | 0.19 | 0.01 | 0.28 | 0.04 | 0.74 | 0.17 | 0.07 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.03 | 0.01 | 0.02 | 0.04 | 0.02 | 0.00 | 0.05 | 0.05 | 0.05 |
| GNAS | ENSG00000087460 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.00 | 0.07 | 0.03 | 0.00 | 0.00 | 0.03 | 0.01 | 0.28 | 0.01 | 0.04 | 0.04 | 0.01 | 0.01 | 0.10 | 0.01 | 0.23 | 0.00 | 0.14 | 0.00 | 0.08 | 0.00 | 0.05 | 0.00 | 0.10 | 0.00 | 0.00 | 0.01 | 0.05 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.37 | 0.02 | 0.38 | 0.05 | 0.03 | 0.03 | 0.09 | 0.01 | 0.17 | 0.00 | 0.26 | 0.04 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.09 | 0.01 |
| BRCA1 | ENSG00000012048 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.09 | 0.04 | 0.02 | 0.01 | 0.01 | 0.02 | 0.03 | 0.06 | 0.01 | 0.03 | 0.05 | 0.03 | 0.02 | 0.17 | 0.02 | 0.10 | 0.04 | 0.03 | 0.01 | 0.03 | 0.03 | 0.04 | 0.02 | 0.05 | 0.04 | 0.02 | 0.01 | 0.03 | 0.14 | 0.02 | 0.10 | 0.00 | 0.00 | 0.05 | 0.11 | 0.02 | 0.17 | 0.04 | 0.03 | 0.02 | 0.08 | 0.02 | 0.19 | 0.04 | 0.09 | 0.02 | 0.01 | 0.00 | 0.01 | 0.02 | 0.06 | 0.00 | 0.01 | 0.01 | 0.03 | 0.00 | 0.05 | 0.01 | 0.03 |
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