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 |
| SLC12A3 | ENSG00000070915 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.05 | 0.01 | 0.04 | 0.00 | 0.03 | 0.00 | 0.01 | 0.05 | 0.03 | 0.04 | 0.02 | 0.03 | 0.03 | 0.10 | 0.01 | 0.01 | 0.03 | 0.01 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.01 | 0.02 | 0.00 | 0.01 | 0.10 | 0.05 | 0.00 | 0.02 | 0.00 | 0.00 | 0.03 | 0.04 | 0.06 | 0.13 | 0.00 | 0.08 | 0.06 | 0.06 | 0.04 | 0.12 | 0.04 | 0.09 | 0.12 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.01 | 0.01 | 0.02 | 0.00 | 0.03 | 0.00 | 0.04 |
| MGAT4A | ENSG00000071073 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 | 0.12 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.05 | 0.01 | 0.15 | 0.01 | 0.09 | 0.01 | 0.21 | 0.01 | 0.06 | 0.01 | 0.01 | 0.00 | 0.04 | 0.01 | 0.00 | 0.01 | 0.01 | 0.01 | 0.00 | 0.01 | 0.03 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.02 | 0.17 | 0.06 | 0.03 | 0.01 | 0.06 | 0.01 | 0.35 | 0.00 | 0.15 | 0.03 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.06 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 |
| WDR1 | ENSG00000071127 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.03 | 0.08 | 0.05 | 0.00 | 0.00 | 0.00 | 0.03 | 0.02 | 0.03 | 0.03 | 0.04 | 0.02 | 0.05 | 0.05 | 0.04 | 0.05 | 0.04 | 0.01 | 0.02 | 0.04 | 0.03 | 0.00 | 0.02 | 0.03 | 0.03 | 0.00 | 0.01 | 0.08 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.04 | 0.22 | 0.06 | 0.01 | 0.03 | 0.05 | 0.02 | 0.13 | 0.00 | 0.07 | 0.05 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.01 | 0.02 | 0.02 | 0.00 | 0.05 | 0.02 |
| ING3 | ENSG00000071243 | 0.01 | 0.01 | 0.08 | 0.00 | 0.01 | 0.00 | 0.03 | 0.04 | 0.04 | 0.03 | 0.00 | 0.01 | 0.05 | 0.02 | 0.06 | 0.02 | 0.10 | 0.05 | 0.04 | 0.09 | 0.06 | 0.17 | 0.08 | 0.06 | 0.02 | 0.00 | 0.00 | 0.02 | 0.03 | 0.03 | 0.09 | 0.03 | 0.00 | 0.02 | 0.00 | 0.06 | 0.00 | 0.02 | 0.00 | 0.00 | 0.07 | 0.03 | 0.29 | 0.06 | 0.03 | 0.05 | 0.02 | 0.05 | 0.09 | 0.09 | 0.10 | 0.03 | 0.03 | 0.02 | 0.00 | 0.03 | 0.09 | 0.07 | 0.09 | 0.01 | 0.05 | 0.00 | 0.00 | 0.00 | 0.17 | 0.02 |
| VASH1 | ENSG00000071246 | 0.01 | 0.03 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.05 | 0.05 | 0.00 | 0.01 | 0.00 | 0.06 | 0.03 | 0.05 | 0.05 | 0.03 | 0.05 | 0.01 | 0.08 | 0.03 | 0.03 | 0.04 | 0.00 | 0.03 | 0.01 | 0.04 | 0.01 | 0.02 | 0.01 | 0.10 | 0.00 | 0.26 | 0.04 | 0.00 | 0.03 | 0.04 | 0.00 | 0.00 | 0.03 | 0.10 | 0.18 | 0.17 | 0.05 | 0.03 | 0.07 | 0.02 | 0.04 | 0.06 | 0.08 | 0.12 | 0.03 | 0.01 | 0.00 | 0.00 | 0.04 | 0.00 | 0.00 | 0.11 | 0.03 | 0.07 | 0.03 | 0.00 | 0.00 | 0.04 |
| TRIB2 | ENSG00000071575 | 0.00 | 0.00 | 0.01 | 0.02 | 0.00 | 0.06 | 0.02 | 0.02 | 0.12 | 0.01 | 0.00 | 0.00 | 0.03 | 0.05 | 0.05 | 0.02 | 0.10 | 0.04 | 0.03 | 0.04 | 0.04 | 0.07 | 0.06 | 0.04 | 0.01 | 0.01 | 0.00 | 0.03 | 0.01 | 0.03 | 0.12 | 0.01 | 0.00 | 0.05 | 0.01 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.05 | 0.22 | 0.15 | 0.08 | 0.01 | 0.09 | 0.03 | 0.24 | 0.03 | 0.04 | 0.12 | 0.16 | 0.01 | 0.00 | 0.00 | 0.03 | 0.03 | 0.01 | 0.01 | 0.05 | 0.01 | 0.05 | 0.00 | 0.02 | 0.04 |
| PRLH | ENSG00000071677 | 0.01 | 0.08 | 0.04 | 0.05 | 0.00 | 0.05 | 0.01 | 0.04 | 0.00 | 0.31 | 0.00 | 0.01 | 0.00 | 0.08 | 0.04 | 0.05 | 0.03 | 0.19 | 0.01 | 0.18 | 0.03 | 0.16 | 0.03 | 0.08 | 0.02 | 0.03 | 0.04 | 0.03 | 0.04 | 0.04 | 0.04 | 0.08 | 0.00 | 0.01 | 0.01 | 0.05 | 0.00 | 0.01 | 0.00 | 0.01 | 0.03 | 0.10 | 0.21 | 0.25 | 0.01 | 0.38 | 0.03 | 0.06 | 0.13 | 0.09 | 0.05 | 0.39 | 0.05 | 0.05 | 0.00 | 0.00 | 0.07 | 0.00 | 0.00 | 0.12 | 0.00 | 0.04 | 0.01 | 0.08 | 0.02 | 0.13 |
| SPP2 | ENSG00000072080 | 0.01 | 0.08 | 0.04 | 0.05 | 0.00 | 0.05 | 0.01 | 0.04 | 0.00 | 0.32 | 0.00 | 0.02 | 0.00 | 0.08 | 0.04 | 0.05 | 0.02 | 0.20 | 0.01 | 0.19 | 0.04 | 0.17 | 0.03 | 0.09 | 0.03 | 0.03 | 0.02 | 0.02 | 0.05 | 0.03 | 0.03 | 0.06 | 0.00 | 0.01 | 0.00 | 0.07 | 0.00 | 0.01 | 0.00 | 0.01 | 0.02 | 0.11 | 0.17 | 0.22 | 0.01 | 0.38 | 0.04 | 0.06 | 0.13 | 0.06 | 0.04 | 0.39 | 0.04 | 0.03 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.11 | 0.00 | 0.04 | 0.01 | 0.08 | 0.01 | 0.12 |
| PTPN18 | ENSG00000072135 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.15 | 0.04 | 0.03 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 | 0.06 | 0.02 | 0.05 | 0.01 | 0.08 | 0.06 | 0.04 | 0.05 | 0.01 | 0.01 | 0.00 | 0.01 | 0.02 | 0.01 | 0.01 | 0.03 | 0.00 | 0.03 | 0.05 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.05 | 0.08 | 0.18 | 0.02 | 0.01 | 0.04 | 0.01 | 0.07 | 0.00 | 0.14 | 0.04 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.12 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 |
| ASIC4 | ENSG00000072182 | 0.01 | 0.07 | 0.04 | 0.04 | 0.00 | 0.03 | 0.01 | 0.03 | 0.01 | 0.27 | 0.00 | 0.02 | 0.00 | 0.10 | 0.02 | 0.03 | 0.04 | 0.19 | 0.00 | 0.18 | 0.04 | 0.13 | 0.05 | 0.04 | 0.02 | 0.01 | 0.02 | 0.02 | 0.05 | 0.03 | 0.03 | 0.04 | 0.00 | 0.04 | 0.03 | 0.03 | 0.01 | 0.00 | 0.00 | 0.01 | 0.04 | 0.06 | 0.18 | 0.16 | 0.03 | 0.35 | 0.05 | 0.04 | 0.08 | 0.05 | 0.09 | 0.20 | 0.08 | 0.01 | 0.00 | 0.00 | 0.00 | 0.04 | 0.00 | 0.02 | 0.00 | 0.01 | 0.02 | 0.02 | 0.02 | 0.05 |
| SPEG | ENSG00000072195 | 0.01 | 0.07 | 0.04 | 0.04 | 0.00 | 0.03 | 0.01 | 0.03 | 0.01 | 0.27 | 0.00 | 0.02 | 0.00 | 0.10 | 0.02 | 0.03 | 0.04 | 0.19 | 0.00 | 0.18 | 0.04 | 0.13 | 0.05 | 0.04 | 0.02 | 0.01 | 0.02 | 0.02 | 0.05 | 0.03 | 0.03 | 0.04 | 0.00 | 0.04 | 0.03 | 0.03 | 0.02 | 0.00 | 0.00 | 0.01 | 0.04 | 0.06 | 0.18 | 0.16 | 0.03 | 0.35 | 0.05 | 0.05 | 0.08 | 0.05 | 0.09 | 0.20 | 0.08 | 0.01 | 0.00 | 0.00 | 0.00 | 0.04 | 0.00 | 0.02 | 0.00 | 0.01 | 0.02 | 0.02 | 0.02 | 0.05 |
| ALDH3A2 | ENSG00000072210 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.15 | 0.06 | 0.00 | 0.01 | 0.00 | 0.02 | 0.08 | 0.04 | 0.09 | 0.04 | 0.03 | 0.03 | 0.07 | 0.08 | 0.04 | 0.05 | 0.02 | 0.02 | 0.01 | 0.07 | 0.08 | 0.01 | 0.10 | 0.04 | 0.09 | 0.01 | 0.10 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.11 | 0.05 | 0.02 | 0.15 | 0.02 | 0.05 | 0.07 | 0.06 | 0.26 | 0.21 | 0.67 | 0.02 | 0.03 | 0.00 | 0.00 | 0.00 | 0.06 | 0.00 | 0.01 | 0.01 | 0.01 | 0.02 | 0.00 | 0.00 | 0.01 | 0.03 |
| TRPC5 | ENSG00000072315 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.04 | 0.03 | 0.03 | 0.00 | 0.00 | 0.01 | 0.04 | 0.01 | 0.10 | 0.01 | 0.04 | 0.01 | 0.08 | 0.02 | 0.06 | 0.02 | 0.02 | 0.01 | 0.02 | 0.01 | 0.01 | 0.00 | 0.02 | 0.01 | 0.03 | 0.01 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.02 | 0.09 | 0.07 | 0.06 | 0.01 | 0.02 | 0.02 | 0.01 | 0.02 | 0.10 | 0.09 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.02 | 0.01 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 |
| HSD17B10 | ENSG00000072506 | 0.01 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.04 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.02 | 0.06 | 0.03 | 0.04 | 0.03 | 0.05 | 0.04 | 0.02 | 0.01 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.29 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.05 | 0.01 | 0.23 | 0.04 | 0.02 | 0.03 | 0.05 | 0.01 | 0.19 | 0.06 | 0.19 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.07 | 0.00 | 0.03 | 0.00 | 0.02 | 0.00 | 0.03 | 0.00 | 0.01 | 0.00 |
| HMMR | ENSG00000072571 | 0.32 | 0.00 | 0.04 | 0.01 | 0.00 | 0.00 | 0.03 | 0.01 | 0.02 | 0.09 | 0.00 | 0.00 | 0.02 | 0.07 | 0.05 | 0.05 | 0.02 | 0.05 | 0.01 | 0.05 | 0.06 | 0.03 | 0.03 | 0.04 | 0.01 | 0.03 | 0.04 | 0.04 | 0.02 | 0.01 | 0.11 | 0.05 | 0.09 | 0.01 | 0.23 | 0.04 | 0.00 | 0.03 | 0.01 | 0.00 | 0.06 | 0.05 | 0.17 | 0.16 | 0.04 | 0.03 | 0.02 | 0.02 | 0.15 | 0.01 | 0.10 | 0.08 | 0.00 | 0.01 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.08 | 0.01 | 0.06 | 0.04 | 0.00 | 0.03 | 0.12 |
| FCGR2B | ENSG00000072694 | 0.03 | 0.00 | 0.01 | 0.01 | 0.00 | 0.03 | 0.02 | 0.04 | 0.79 | 0.01 | 0.02 | 0.00 | 0.10 | 0.01 | 0.27 | 0.00 | 0.27 | 0.00 | 0.05 | 0.00 | 0.29 | 0.01 | 0.13 | 0.00 | 0.03 | 0.00 | 0.14 | 0.00 | 0.06 | 0.00 | 0.29 | 0.00 | 0.30 | 0.01 | 0.16 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.31 | 0.01 | 0.37 | 0.02 | 0.17 | 0.00 | 0.13 | 0.00 | 0.28 | 0.00 | 0.34 | 0.03 | 0.10 | 0.00 | 0.00 | 0.00 | 0.25 | 0.00 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.18 | 0.01 |
| CYP2W1 | ENSG00000073067 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.03 | 0.14 | 0.04 | 0.00 | 0.00 | 0.10 | 0.00 | 0.11 | 0.01 | 0.15 | 0.04 | 0.13 | 0.02 | 0.25 | 0.04 | 0.15 | 0.03 | 0.05 | 0.01 | 0.04 | 0.01 | 0.06 | 0.00 | 0.07 | 0.02 | 0.01 | 0.01 | 0.16 | 0.03 | 0.00 | 0.01 | 0.00 | 0.00 | 0.09 | 0.07 | 0.15 | 0.40 | 0.06 | 0.02 | 0.06 | 0.07 | 0.28 | 0.05 | 0.13 | 0.06 | 0.15 | 0.01 | 0.00 | 0.01 | 0.15 | 0.00 | 0.01 | 0.04 | 0.05 | 0.01 | 0.00 | 0.00 | 0.15 | 0.01 |
| ADAM11 | ENSG00000073670 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.14 | 0.04 | 0.03 | 0.01 | 0.00 | 0.03 | 0.00 | 0.06 | 0.01 | 0.05 | 0.05 | 0.01 | 0.01 | 0.14 | 0.03 | 0.07 | 0.02 | 0.03 | 0.00 | 0.03 | 0.03 | 0.05 | 0.01 | 0.02 | 0.03 | 0.02 | 0.01 | 0.01 | 0.11 | 0.00 | 0.08 | 0.00 | 0.00 | 0.03 | 0.10 | 0.02 | 0.11 | 0.02 | 0.02 | 0.03 | 0.07 | 0.05 | 0.18 | 0.05 | 0.08 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.01 | 0.00 | 0.05 | 0.02 | 0.05 |
| DHRS9 | ENSG00000073737 | 0.02 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.01 | 0.09 | 0.07 | 0.04 | 0.00 | 0.01 | 0.00 | 0.00 | 0.06 | 0.01 | 0.09 | 0.02 | 0.08 | 0.01 | 0.10 | 0.02 | 0.05 | 0.04 | 0.01 | 0.01 | 0.01 | 0.02 | 0.02 | 0.01 | 0.05 | 0.06 | 0.00 | 0.01 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.03 | 0.31 | 0.05 | 0.08 | 0.01 | 0.05 | 0.01 | 0.06 | 0.00 | 0.04 | 0.08 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.07 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.02 |
| CD5L | ENSG00000073754 | 0.03 | 0.00 | 0.01 | 0.01 | 0.00 | 0.03 | 0.02 | 0.06 | 0.40 | 0.01 | 0.02 | 0.00 | 0.11 | 0.00 | 0.26 | 0.00 | 0.24 | 0.01 | 0.07 | 0.00 | 0.25 | 0.00 | 0.12 | 0.00 | 0.03 | 0.00 | 0.11 | 0.00 | 0.07 | 0.00 | 0.30 | 0.00 | 0.41 | 0.01 | 0.05 | 0.02 | 0.04 | 0.00 | 0.00 | 0.00 | 0.28 | 0.01 | 0.39 | 0.02 | 0.16 | 0.00 | 0.15 | 0.00 | 0.37 | 0.00 | 0.41 | 0.01 | 0.10 | 0.00 | 0.00 | 0.00 | 0.25 | 0.00 | 0.01 | 0.00 | 0.05 | 0.00 | 0.00 | 0.03 | 0.18 | 0.01 |
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