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 |
| LAMP2 | ENSG00000005893 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.03 | 0.03 | 0.01 | 0.03 | 0.01 | 0.09 | 0.01 | 0.09 | 0.01 | 0.05 | 0.01 | 0.14 | 0.02 | 0.08 | 0.01 | 0.03 | 0.01 | 0.02 | 0.02 | 0.01 | 0.00 | 0.07 | 0.02 | 0.03 | 0.01 | 0.07 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.02 | 0.18 | 0.03 | 0.04 | 0.01 | 0.02 | 0.01 | 0.01 | 0.05 | 0.07 | 0.10 | 0.00 | 0.02 | 0.00 | 0.00 | 0.02 | 0.02 | 0.00 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.03 | 0.01 |
| ITGA2B | ENSG00000005961 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.17 | 0.04 | 0.03 | 0.01 | 0.00 | 0.03 | 0.00 | 0.06 | 0.01 | 0.04 | 0.05 | 0.01 | 0.01 | 0.12 | 0.03 | 0.06 | 0.03 | 0.02 | 0.00 | 0.03 | 0.03 | 0.05 | 0.01 | 0.02 | 0.03 | 0.02 | 0.01 | 0.01 | 0.13 | 0.02 | 0.09 | 0.00 | 0.00 | 0.04 | 0.10 | 0.02 | 0.13 | 0.03 | 0.03 | 0.03 | 0.07 | 0.10 | 0.16 | 0.06 | 0.06 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.05 | 0.00 | 0.01 | 0.01 | 0.02 | 0.00 | 0.05 | 0.01 | 0.05 |
| MAP3K14 | ENSG00000006062 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.12 | 0.03 | 0.02 | 0.01 | 0.00 | 0.03 | 0.00 | 0.05 | 0.01 | 0.09 | 0.04 | 0.01 | 0.01 | 0.12 | 0.03 | 0.09 | 0.01 | 0.02 | 0.00 | 0.03 | 0.03 | 0.04 | 0.01 | 0.03 | 0.03 | 0.02 | 0.01 | 0.07 | 0.08 | 0.00 | 0.06 | 0.00 | 0.00 | 0.03 | 0.10 | 0.02 | 0.12 | 0.07 | 0.02 | 0.04 | 0.07 | 0.05 | 0.18 | 0.06 | 0.07 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.01 | 0.00 | 0.05 | 0.01 | 0.05 |
| TAC1 | ENSG00000006128 | 0.01 | 0.00 | 0.05 | 0.00 | 0.00 | 0.00 | 0.05 | 0.00 | 0.05 | 0.01 | 0.00 | 0.00 | 0.03 | 0.00 | 0.11 | 0.01 | 0.22 | 0.01 | 0.23 | 0.00 | 0.56 | 0.02 | 0.34 | 0.01 | 0.04 | 0.01 | 0.01 | 0.01 | 0.06 | 0.02 | 0.08 | 0.02 | 0.11 | 0.01 | 0.10 | 0.03 | 0.00 | 0.02 | 0.00 | 0.00 | 0.06 | 0.03 | 0.18 | 0.06 | 0.05 | 0.01 | 0.07 | 0.01 | 0.08 | 0.04 | 0.07 | 0.04 | 0.11 | 0.00 | 0.00 | 0.00 | 0.13 | 0.00 | 0.05 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.05 | 0.02 |
| TNFRSF12A | ENSG00000006327 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.01 | 0.17 | 0.00 | 0.00 | 0.04 | 0.02 | 0.04 | 0.03 | 0.04 | 0.09 | 0.04 | 0.03 | 0.03 | 0.08 | 0.03 | 0.08 | 0.03 | 0.03 | 0.03 | 0.02 | 0.01 | 0.02 | 0.03 | 0.02 | 0.05 | 0.05 | 0.11 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.08 | 0.02 | 0.09 | 0.19 | 0.10 | 0.02 | 0.05 | 0.04 | 0.08 | 0.05 | 0.09 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.00 | 0.01 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.05 | 0.01 |
| MAP3K9 | ENSG00000006432 | 0.01 | 0.03 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.04 | 0.05 | 0.05 | 0.00 | 0.01 | 0.00 | 0.05 | 0.03 | 0.04 | 0.03 | 0.05 | 0.03 | 0.02 | 0.05 | 0.03 | 0.03 | 0.05 | 0.00 | 0.03 | 0.01 | 0.03 | 0.02 | 0.01 | 0.00 | 0.09 | 0.00 | 0.33 | 0.00 | 0.05 | 0.01 | 0.04 | 0.00 | 0.00 | 0.01 | 0.11 | 0.07 | 0.25 | 0.02 | 0.02 | 0.01 | 0.02 | 0.05 | 0.04 | 0.05 | 0.12 | 0.02 | 0.01 | 0.00 | 0.00 | 0.04 | 0.00 | 0.00 | 0.11 | 0.01 | 0.07 | 0.03 | 0.00 | 0.01 | 0.04 |
| KDM7A | ENSG00000006459 | 0.02 | 0.01 | 0.05 | 0.00 | 0.05 | 0.02 | 0.03 | 0.02 | 0.04 | 0.04 | 0.00 | 0.01 | 0.04 | 0.05 | 0.08 | 0.02 | 0.09 | 0.06 | 0.03 | 0.14 | 0.04 | 0.19 | 0.05 | 0.08 | 0.03 | 0.00 | 0.03 | 0.02 | 0.04 | 0.04 | 0.05 | 0.04 | 0.00 | 0.06 | 0.06 | 0.06 | 0.00 | 0.01 | 0.00 | 0.00 | 0.10 | 0.04 | 0.53 | 0.04 | 0.04 | 0.08 | 0.06 | 0.05 | 0.08 | 0.14 | 0.09 | 0.09 | 0.02 | 0.04 | 0.00 | 0.05 | 0.02 | 0.09 | 0.12 | 0.00 | 0.05 | 0.01 | 0.00 | 0.00 | 0.24 | 0.02 |
| ALDH3B1 | ENSG00000006534 | 0.01 | 0.00 | 0.03 | 0.01 | 0.08 | 0.02 | 0.10 | 0.00 | 0.28 | 0.01 | 0.00 | 0.00 | 0.08 | 0.00 | 0.15 | 0.01 | 0.21 | 0.02 | 0.41 | 0.02 | 0.63 | 0.02 | 0.14 | 0.03 | 0.02 | 0.01 | 0.05 | 0.02 | 0.03 | 0.01 | 0.18 | 0.02 | 0.19 | 0.01 | 0.03 | 0.03 | 0.03 | 0.00 | 0.00 | 0.00 | 0.46 | 0.04 | 0.30 | 0.03 | 0.18 | 0.01 | 0.17 | 0.02 | 0.17 | 0.04 | 0.09 | 0.03 | 0.00 | 0.05 | 0.00 | 0.00 | 0.00 | 0.06 | 0.01 | 0.01 | 0.02 | 0.04 | 0.00 | 0.00 | 0.25 | 0.02 |
| CCL26 | ENSG00000006606 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.04 | 0.02 | 0.00 | 0.00 | 0.02 | 0.00 | 0.02 | 0.02 | 0.08 | 0.02 | 0.05 | 0.03 | 0.13 | 0.02 | 0.11 | 0.01 | 0.01 | 0.01 | 0.01 | 0.00 | 0.03 | 0.00 | 0.05 | 0.01 | 0.00 | 0.01 | 0.13 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.06 | 0.02 | 0.17 | 0.08 | 0.05 | 0.01 | 0.04 | 0.02 | 0.10 | 0.03 | 0.05 | 0.07 | 0.09 | 0.00 | 0.00 | 0.00 | 0.10 | 0.00 | 0.02 | 0.01 | 0.08 | 0.00 | 0.00 | 0.00 | 0.05 | 0.02 |
| DBF4 | ENSG00000006634 | 0.01 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.04 | 0.00 | 0.05 | 0.01 | 0.00 | 0.00 | 0.03 | 0.03 | 0.03 | 0.01 | 0.21 | 0.02 | 0.19 | 0.01 | 0.49 | 0.02 | 0.24 | 0.01 | 0.03 | 0.01 | 0.01 | 0.00 | 0.05 | 0.00 | 0.06 | 0.03 | 0.04 | 0.01 | 0.10 | 0.02 | 0.00 | 0.02 | 0.00 | 0.00 | 0.06 | 0.02 | 0.18 | 0.05 | 0.09 | 0.02 | 0.02 | 0.02 | 0.09 | 0.06 | 0.06 | 0.05 | 0.13 | 0.00 | 0.00 | 0.00 | 0.13 | 0.00 | 0.02 | 0.00 | 0.05 | 0.01 | 0.00 | 0.00 | 0.02 | 0.02 |
| TBXA2R | ENSG00000006638 | 0.00 | 0.01 | 0.00 | 0.02 | 0.00 | 0.02 | 0.00 | 0.06 | 0.04 | 0.13 | 0.02 | 0.00 | 0.01 | 0.10 | 0.01 | 0.09 | 0.02 | 0.11 | 0.03 | 0.11 | 0.08 | 0.12 | 0.00 | 0.09 | 0.01 | 0.05 | 0.01 | 0.10 | 0.01 | 0.06 | 0.02 | 0.14 | 0.00 | 0.03 | 0.04 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.05 | 0.12 | 0.03 | 0.87 | 0.08 | 0.19 | 0.00 | 0.28 | 0.00 | 0.78 | 0.17 | 0.09 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.03 | 0.02 | 0.02 | 0.04 | 0.01 | 0.01 | 0.02 | 0.03 | 0.06 |
| ARSD | ENSG00000006756 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.04 | 0.01 | 0.08 | 0.07 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.07 | 0.11 | 0.07 | 0.03 | 0.03 | 0.07 | 0.12 | 0.07 | 0.04 | 0.02 | 0.02 | 0.07 | 0.08 | 0.00 | 0.00 | 0.02 | 0.04 | 0.02 | 0.01 | 0.11 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.06 | 0.05 | 0.20 | 0.20 | 0.09 | 0.02 | 0.05 | 0.04 | 0.09 | 0.11 | 0.21 | 0.11 | 0.05 | 0.02 | 0.00 | 0.00 | 0.00 | 0.07 | 0.04 | 0.02 | 0.02 | 0.01 | 0.00 | 0.01 | 0.04 | 0.02 |
| PRSS21 | ENSG00000007038 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.01 | 0.15 | 0.00 | 0.00 | 0.04 | 0.02 | 0.04 | 0.03 | 0.03 | 0.09 | 0.04 | 0.03 | 0.05 | 0.08 | 0.03 | 0.08 | 0.03 | 0.03 | 0.03 | 0.02 | 0.01 | 0.02 | 0.03 | 0.02 | 0.00 | 0.05 | 0.11 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.09 | 0.02 | 0.10 | 0.16 | 0.10 | 0.02 | 0.06 | 0.04 | 0.03 | 0.05 | 0.09 | 0.03 | 0.01 | 0.00 | 0.00 | 0.00 | 0.09 | 0.00 | 0.01 | 0.00 | 0.04 | 0.01 | 0.00 | 0.00 | 0.05 | 0.01 |
| PROM1 | ENSG00000007062 | 0.01 | 0.00 | 0.01 | 0.00 | 0.02 | 0.00 | 0.02 | 0.04 | 0.04 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.02 | 0.03 | 0.06 | 0.02 | 0.05 | 0.04 | 0.03 | 0.04 | 0.04 | 0.01 | 0.02 | 0.03 | 0.03 | 0.00 | 0.02 | 0.05 | 0.03 | 0.00 | 0.01 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.04 | 0.16 | 0.06 | 0.01 | 0.01 | 0.08 | 0.02 | 0.19 | 0.00 | 0.07 | 0.04 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.01 | 0.02 | 0.05 | 0.00 | 0.03 | 0.01 |
| SCN4A | ENSG00000007314 | 0.02 | 0.00 | 0.05 | 0.00 | 0.00 | 0.00 | 0.03 | 0.02 | 0.25 | 0.01 | 0.02 | 0.00 | 0.12 | 0.00 | 0.14 | 0.01 | 0.20 | 0.01 | 0.07 | 0.02 | 0.22 | 0.02 | 0.11 | 0.02 | 0.07 | 0.01 | 0.07 | 0.02 | 0.08 | 0.10 | 0.20 | 0.00 | 0.12 | 0.01 | 0.17 | 0.03 | 0.02 | 0.00 | 0.00 | 0.00 | 0.58 | 0.01 | 0.24 | 0.03 | 0.17 | 0.02 | 0.10 | 0.03 | 0.27 | 0.02 | 0.17 | 0.03 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.06 | 0.06 | 0.00 | 0.03 | 0.01 | 0.16 | 0.00 | 0.24 | 0.01 |
| SELE | ENSG00000007908 | 0.03 | 0.00 | 0.01 | 0.01 | 0.00 | 0.03 | 0.01 | 0.05 | 0.44 | 0.01 | 0.02 | 0.02 | 0.10 | 0.03 | 0.14 | 0.01 | 0.24 | 0.01 | 0.04 | 0.00 | 0.21 | 0.01 | 0.11 | 0.01 | 0.03 | 0.00 | 0.11 | 0.00 | 0.06 | 0.00 | 0.23 | 0.00 | 0.22 | 0.05 | 0.00 | 0.04 | 0.04 | 0.00 | 0.00 | 0.00 | 0.20 | 0.02 | 0.33 | 0.02 | 0.11 | 0.00 | 0.10 | 0.00 | 0.29 | 0.00 | 0.50 | 0.03 | 0.10 | 0.00 | 0.00 | 0.00 | 0.36 | 0.04 | 0.01 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.15 | 0.01 |
| NOX1 | ENSG00000007952 | 0.01 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.06 | 0.02 | 0.00 | 0.00 | 0.00 | 0.01 | 0.03 | 0.02 | 0.07 | 0.01 | 0.04 | 0.01 | 0.14 | 0.02 | 0.05 | 0.01 | 0.02 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.03 | 0.06 | 0.05 | 0.03 | 0.01 | 0.02 | 0.02 | 0.01 | 0.02 | 0.07 | 0.09 | 0.00 | 0.01 | 0.00 | 0.00 | 0.04 | 0.02 | 0.02 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 |
| PSMB1 | ENSG00000008018 | 0.00 | 0.05 | 0.00 | 0.02 | 0.00 | 0.05 | 0.00 | 0.04 | 0.04 | 0.08 | 0.00 | 0.01 | 0.04 | 0.09 | 0.02 | 0.06 | 0.10 | 0.07 | 0.06 | 0.05 | 0.12 | 0.05 | 0.11 | 0.08 | 0.02 | 0.02 | 0.03 | 0.02 | 0.01 | 0.05 | 0.02 | 0.15 | 0.06 | 0.18 | 0.12 | 0.05 | 0.01 | 0.04 | 0.01 | 0.00 | 0.06 | 0.13 | 0.08 | 0.47 | 0.02 | 0.10 | 0.04 | 0.05 | 0.21 | 0.08 | 0.15 | 0.12 | 0.01 | 0.05 | 0.01 | 0.01 | 0.03 | 0.09 | 0.00 | 0.05 | 0.03 | 0.09 | 0.00 | 0.06 | 0.03 | 0.15 |
| CDKL5 | ENSG00000008086 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.06 | 0.01 | 0.04 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.04 | 0.11 | 0.04 | 0.03 | 0.02 | 0.09 | 0.04 | 0.03 | 0.02 | 0.00 | 0.01 | 0.10 | 0.00 | 0.00 | 0.00 | 0.02 | 0.02 | 0.00 | 0.01 | 0.12 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.06 | 0.03 | 0.11 | 0.14 | 0.06 | 0.02 | 0.04 | 0.02 | 0.10 | 0.07 | 0.13 | 0.04 | 0.07 | 0.01 | 0.00 | 0.00 | 0.04 | 0.04 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.04 | 0.02 |
| CAMK1G | ENSG00000008118 | 0.01 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.04 | 0.07 | 0.06 | 0.01 | 0.00 | 0.07 | 0.01 | 0.10 | 0.01 | 0.11 | 0.01 | 0.06 | 0.01 | 0.16 | 0.05 | 0.04 | 0.02 | 0.03 | 0.01 | 0.09 | 0.03 | 0.01 | 0.00 | 0.15 | 0.02 | 0.16 | 0.02 | 0.01 | 0.03 | 0.02 | 0.00 | 0.00 | 0.00 | 0.23 | 0.01 | 0.17 | 0.15 | 0.06 | 0.00 | 0.07 | 0.02 | 0.13 | 0.04 | 0.03 | 0.20 | 0.02 | 0.03 | 0.01 | 0.00 | 0.16 | 0.04 | 0.00 | 0.01 | 0.04 | 0.03 | 0.09 | 0.00 | 0.12 | 0.02 |
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