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 |
| DHCR7 | ENSG00000172893 | 0.01 | 0.00 | 0.01 | 0.01 | 0.09 | 0.00 | 0.04 | 0.01 | 0.31 | 0.03 | 0.00 | 0.00 | 0.08 | 0.00 | 0.14 | 0.01 | 0.48 | 0.02 | 1.07 | 0.03 | 1.40 | 0.00 | 0.17 | 0.02 | 0.01 | 0.01 | 0.02 | 0.02 | 0.02 | 0.02 | 0.10 | 0.03 | 0.00 | 0.06 | 0.01 | 0.01 | 0.02 | 0.00 | 0.00 | 0.00 | 0.57 | 0.04 | 0.44 | 0.04 | 0.19 | 0.01 | 0.10 | 0.02 | 0.18 | 0.11 | 0.10 | 0.07 | 0.00 | 0.06 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.25 | 0.01 |
| WNK1 | ENSG00000060237 | 0.02 | 0.00 | 0.00 | 0.01 | 0.04 | 0.02 | 0.01 | 0.06 | 0.12 | 0.04 | 0.01 | 0.00 | 0.04 | 0.01 | 0.11 | 0.07 | 0.23 | 0.02 | 0.19 | 0.01 | 0.26 | 0.05 | 0.11 | 0.06 | 0.14 | 0.01 | 0.15 | 0.03 | 0.14 | 0.04 | 0.04 | 0.05 | 0.30 | 0.08 | 0.06 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.19 | 0.05 | 0.47 | 0.10 | 0.06 | 0.03 | 0.11 | 0.04 | 0.32 | 0.10 | 0.22 | 0.14 | 0.60 | 0.00 | 0.00 | 0.01 | 0.02 | 0.03 | 0.13 | 0.03 | 0.06 | 0.02 | 0.00 | 0.04 | 0.08 | 0.03 |
| TYR | ENSG00000077498 | 0.01 | 0.01 | 0.00 | 0.03 | 0.02 | 0.03 | 0.03 | 0.02 | 0.10 | 0.05 | 0.00 | 0.00 | 0.06 | 0.07 | 0.11 | 0.02 | 0.10 | 0.05 | 0.11 | 0.07 | 0.19 | 0.04 | 0.04 | 0.03 | 0.02 | 0.00 | 0.01 | 0.03 | 0.02 | 0.01 | 0.03 | 0.04 | 0.00 | 0.02 | 0.00 | 0.02 | 0.00 | 0.04 | 0.00 | 0.00 | 0.13 | 0.09 | 0.39 | 0.07 | 0.13 | 0.06 | 0.07 | 0.03 | 0.06 | 0.19 | 0.08 | 0.10 | 0.04 | 0.07 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.03 | 0.01 | 0.00 | 0.00 | 0.11 | 0.07 |
| AFG3L2 | ENSG00000141385 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.05 | 0.02 | 0.00 | 0.00 | 0.00 | 0.02 | 0.05 | 0.01 | 0.05 | 0.02 | 0.02 | 0.01 | 0.04 | 0.03 | 0.06 | 0.02 | 0.01 | 0.02 | 0.03 | 0.01 | 0.02 | 0.01 | 0.01 | 0.00 | 0.00 | 0.08 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.02 | 0.06 | 0.05 | 0.01 | 0.02 | 0.02 | 0.00 | 0.06 | 0.00 | 0.07 | 0.03 | 0.02 | 0.02 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 |
| RASGRP3 | ENSG00000152689 | 0.00 | 0.00 | 0.01 | 0.02 | 0.00 | 0.00 | 0.02 | 0.06 | 0.08 | 0.00 | 0.00 | 0.00 | 0.03 | 0.08 | 0.06 | 0.02 | 0.09 | 0.02 | 0.03 | 0.01 | 0.04 | 0.04 | 0.02 | 0.04 | 0.00 | 0.01 | 0.00 | 0.03 | 0.01 | 0.03 | 0.07 | 0.00 | 0.00 | 0.05 | 0.00 | 0.04 | 0.00 | 0.01 | 0.00 | 0.00 | 0.06 | 0.02 | 0.22 | 0.06 | 0.08 | 0.00 | 0.08 | 0.02 | 0.21 | 0.00 | 0.08 | 0.05 | 0.12 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.00 | 0.01 | 0.01 | 0.03 | 0.00 | 0.02 | 0.02 |
| RPN2 | ENSG00000118705 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.02 | 0.03 | 0.07 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.02 | 0.11 | 0.01 | 0.05 | 0.01 | 0.11 | 0.01 | 0.08 | 0.00 | 0.07 | 0.00 | 0.18 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.00 | 0.04 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.10 | 0.02 | 0.10 | 0.06 | 0.05 | 0.01 | 0.06 | 0.01 | 0.21 | 0.00 | 0.07 | 0.05 | 0.00 | 0.01 | 0.00 | 0.03 | 0.01 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.05 | 0.00 |
| INSR | ENSG00000171105 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.02 | 0.02 | 0.03 | 0.07 | 0.08 | 0.00 | 0.01 | 0.01 | 0.07 | 0.01 | 0.06 | 0.06 | 0.09 | 0.01 | 0.08 | 0.03 | 0.13 | 0.02 | 0.08 | 0.03 | 0.02 | 0.04 | 0.05 | 0.02 | 0.04 | 0.01 | 0.11 | 0.00 | 0.01 | 0.17 | 0.03 | 0.01 | 0.00 | 0.00 | 0.01 | 0.09 | 0.07 | 0.25 | 0.48 | 0.03 | 0.17 | 0.04 | 0.22 | 0.04 | 0.56 | 0.36 | 0.02 | 0.02 | 0.00 | 0.04 | 0.00 | 0.00 | 0.11 | 0.01 | 0.01 | 0.03 | 0.01 | 0.00 | 0.05 | 0.05 | 0.03 |
| PRKCB | ENSG00000166501 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.17 | 0.03 | 0.00 | 0.00 | 0.02 | 0.04 | 0.03 | 0.01 | 0.07 | 0.02 | 0.04 | 0.02 | 0.03 | 0.01 | 0.01 | 0.00 | 0.02 | 0.01 | 0.01 | 0.00 | 0.01 | 0.00 | 0.05 | 0.01 | 0.01 | 0.02 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.04 | 0.01 | 0.07 | 0.06 | 0.01 | 0.01 | 0.03 | 0.01 | 0.17 | 0.03 | 0.01 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.18 | 0.00 | 0.00 | 0.02 | 0.00 | 0.07 | 0.00 | 0.00 | 0.01 | 0.02 |
| KRT8 | ENSG00000170421 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.00 | 0.02 | 0.00 | 0.06 | 0.03 | 0.00 | 0.00 | 0.00 | 0.04 | 0.07 | 0.01 | 0.04 | 0.02 | 0.01 | 0.03 | 0.05 | 0.03 | 0.07 | 0.04 | 0.02 | 0.00 | 0.03 | 0.01 | 0.01 | 0.03 | 0.03 | 0.01 | 0.34 | 0.01 | 0.16 | 0.00 | 0.03 | 0.01 | 0.00 | 0.00 | 0.04 | 0.06 | 0.14 | 0.05 | 0.03 | 0.00 | 0.09 | 0.01 | 0.46 | 0.04 | 0.02 | 0.10 | 0.01 | 0.00 | 0.00 | 0.00 | 0.12 | 0.00 | 0.00 | 0.03 | 0.05 | 0.04 | 0.00 | 0.00 | 0.02 | 0.06 |
| PIK3R1 | ENSG00000145675 | 0.00 | 0.01 | 0.00 | 0.01 | 0.03 | 0.01 | 0.00 | 0.21 | 0.01 | 0.18 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.08 | 0.01 | 0.10 | 0.01 | 0.08 | 0.02 | 0.16 | 0.01 | 0.13 | 0.00 | 0.08 | 0.00 | 0.10 | 0.00 | 0.07 | 0.01 | 0.05 | 0.00 | 0.13 | 0.08 | 0.00 | 0.01 | 0.03 | 0.00 | 0.00 | 0.01 | 0.11 | 0.01 | 0.71 | 0.00 | 0.07 | 0.02 | 0.12 | 0.04 | 0.36 | 0.03 | 0.06 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.04 | 0.00 | 0.00 | 0.04 | 0.04 |
| CFTR | ENSG00000001626 | 0.02 | 0.01 | 0.10 | 0.00 | 0.01 | 0.00 | 0.02 | 0.04 | 0.08 | 0.03 | 0.00 | 0.01 | 0.03 | 0.03 | 0.13 | 0.02 | 0.13 | 0.05 | 0.06 | 0.07 | 0.18 | 0.16 | 0.19 | 0.06 | 0.03 | 0.01 | 0.04 | 0.02 | 0.01 | 0.03 | 0.13 | 0.03 | 0.00 | 0.06 | 0.02 | 0.06 | 0.00 | 0.02 | 0.00 | 0.00 | 0.06 | 0.04 | 0.34 | 0.07 | 0.04 | 0.05 | 0.11 | 0.04 | 0.23 | 0.09 | 0.12 | 0.03 | 0.03 | 0.02 | 0.00 | 0.03 | 0.09 | 0.04 | 0.10 | 0.00 | 0.06 | 0.00 | 0.00 | 0.00 | 0.13 | 0.02 |
| WDR5 | ENSG00000196363 | 0.00 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.03 | 0.01 | 0.04 | 0.03 | 0.00 | 0.01 | 0.00 | 0.02 | 0.05 | 0.03 | 0.08 | 0.02 | 0.07 | 0.03 | 0.12 | 0.04 | 0.12 | 0.01 | 0.02 | 0.01 | 0.05 | 0.04 | 0.01 | 0.00 | 0.10 | 0.04 | 0.06 | 0.01 | 0.12 | 0.04 | 0.01 | 0.01 | 0.00 | 0.00 | 0.05 | 0.06 | 0.07 | 0.25 | 0.07 | 0.01 | 0.01 | 0.06 | 0.08 | 0.14 | 0.06 | 0.15 | 0.03 | 0.03 | 0.01 | 0.00 | 0.05 | 0.00 | 0.02 | 0.01 | 0.04 | 0.04 | 0.00 | 0.00 | 0.03 | 0.02 |
| PGD | ENSG00000142657 | 0.00 | 0.06 | 0.00 | 0.08 | 0.00 | 0.00 | 0.01 | 0.06 | 0.10 | 0.09 | 0.00 | 0.02 | 0.04 | 0.27 | 0.06 | 0.05 | 0.05 | 0.12 | 0.04 | 0.08 | 0.14 | 0.10 | 0.13 | 0.08 | 0.01 | 0.13 | 0.00 | 0.21 | 0.03 | 0.07 | 0.02 | 0.25 | 0.00 | 1.07 | 0.03 | 0.21 | 0.01 | 0.09 | 0.00 | 0.00 | 0.02 | 0.20 | 0.23 | 0.34 | 0.04 | 0.10 | 0.08 | 0.11 | 0.07 | 0.26 | 0.18 | 0.21 | 0.08 | 0.09 | 0.02 | 0.01 | 0.00 | 0.05 | 0.00 | 0.04 | 0.05 | 0.19 | 0.00 | 0.07 | 0.06 | 0.11 |
| COL6A2 | ENSG00000142173 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.08 | 0.00 | 0.04 | 0.07 | 0.04 | 0.00 | 0.02 | 0.02 | 0.01 | 0.06 | 0.02 | 0.07 | 0.06 | 0.03 | 0.06 | 0.07 | 0.08 | 0.02 | 0.06 | 0.01 | 0.02 | 0.02 | 0.09 | 0.01 | 0.01 | 0.03 | 0.03 | 0.05 | 0.07 | 0.01 | 0.06 | 0.01 | 0.00 | 0.00 | 0.00 | 0.12 | 0.02 | 0.21 | 0.18 | 0.05 | 0.05 | 0.04 | 0.03 | 0.06 | 0.16 | 0.15 | 0.17 | 0.04 | 0.01 | 0.10 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.03 | 0.03 | 0.00 | 0.02 | 0.04 |
| ITGAV | ENSG00000138448 | 0.03 | 0.01 | 0.06 | 0.00 | 0.00 | 0.00 | 0.01 | 0.07 | 0.07 | 0.11 | 0.00 | 0.00 | 0.00 | 0.02 | 0.05 | 0.01 | 0.14 | 0.04 | 0.14 | 0.10 | 0.16 | 0.09 | 0.07 | 0.16 | 0.02 | 0.02 | 0.02 | 0.05 | 0.03 | 0.02 | 0.07 | 0.03 | 0.00 | 0.01 | 0.02 | 0.05 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.02 | 0.41 | 0.05 | 0.12 | 0.06 | 0.09 | 0.01 | 0.00 | 0.03 | 0.05 | 0.09 | 0.06 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.03 | 0.02 |
| HRH1 | ENSG00000196639 | 0.00 | 0.19 | 0.00 | 0.01 | 0.07 | 0.00 | 0.00 | 0.05 | 0.48 | 0.03 | 0.00 | 0.03 | 0.03 | 0.06 | 0.03 | 0.05 | 0.02 | 0.07 | 0.01 | 0.03 | 0.04 | 0.07 | 0.07 | 0.06 | 0.00 | 0.04 | 0.03 | 0.06 | 0.01 | 0.02 | 0.06 | 0.01 | 0.00 | 0.18 | 0.07 | 0.01 | 0.00 | 0.04 | 0.00 | 0.00 | 0.11 | 0.03 | 0.14 | 0.22 | 0.02 | 0.01 | 0.06 | 0.03 | 0.09 | 0.14 | 0.23 | 0.04 | 0.04 | 0.05 | 0.00 | 0.00 | 0.00 | 0.05 | 0.03 | 0.01 | 0.01 | 0.02 | 0.00 | 0.00 | 0.01 | 0.05 |
| SENP6 | ENSG00000112701 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.16 | 0.02 | 0.07 | 0.00 | 0.00 | 0.03 | 0.05 | 0.04 | 0.05 | 0.08 | 0.03 | 0.03 | 0.03 | 0.05 | 0.06 | 0.06 | 0.06 | 0.00 | 0.02 | 0.02 | 0.00 | 0.01 | 0.02 | 0.02 | 0.04 | 0.00 | 0.22 | 0.06 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.08 | 0.17 | 0.10 | 0.01 | 0.01 | 0.07 | 0.01 | 0.17 | 0.12 | 0.03 | 0.17 | 0.03 | 0.00 | 0.00 | 0.00 | 0.01 | 0.14 | 0.01 | 0.01 | 0.00 | 0.04 | 0.08 | 0.05 | 0.02 | 0.04 |
| LGR4 | ENSG00000205213 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.05 | 0.05 | 0.00 | 0.00 | 0.00 | 0.04 | 0.05 | 0.02 | 0.05 | 0.04 | 0.03 | 0.03 | 0.20 | 0.03 | 0.06 | 0.03 | 0.03 | 0.01 | 0.00 | 0.02 | 0.01 | 0.02 | 0.03 | 0.01 | 0.00 | 0.01 | 0.02 | 0.01 | 0.02 | 0.04 | 0.00 | 0.00 | 0.07 | 0.03 | 0.12 | 0.12 | 0.00 | 0.04 | 0.04 | 0.03 | 0.10 | 0.12 | 0.05 | 0.08 | 0.01 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.01 |
| CAT | ENSG00000121691 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.03 | 0.16 | 0.04 | 0.00 | 0.00 | 0.00 | 0.04 | 0.08 | 0.02 | 0.10 | 0.02 | 0.15 | 0.00 | 0.31 | 0.02 | 0.17 | 0.01 | 0.01 | 0.01 | 0.01 | 0.00 | 0.02 | 0.01 | 0.03 | 0.00 | 0.00 | 0.02 | 0.02 | 0.01 | 0.02 | 0.04 | 0.00 | 0.00 | 0.16 | 0.01 | 0.25 | 0.05 | 0.09 | 0.00 | 0.04 | 0.02 | 0.17 | 0.05 | 0.12 | 0.09 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.01 | 0.00 | 0.00 | 0.04 | 0.02 |
| RELB | ENSG00000104856 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.03 | 0.13 | 0.02 | 0.00 | 0.00 | 0.03 | 0.05 | 0.13 | 0.04 | 0.11 | 0.08 | 0.07 | 0.02 | 0.07 | 0.05 | 0.12 | 0.02 | 0.01 | 0.02 | 0.01 | 0.02 | 0.09 | 0.02 | 0.06 | 0.04 | 0.12 | 0.03 | 0.16 | 0.03 | 0.00 | 0.02 | 0.00 | 0.00 | 0.08 | 0.05 | 0.14 | 0.30 | 0.17 | 0.04 | 0.12 | 0.04 | 0.30 | 0.17 | 0.07 | 0.17 | 0.00 | 0.04 | 0.01 | 0.00 | 0.05 | 0.05 | 0.02 | 0.13 | 0.02 | 0.10 | 0.00 | 0.00 | 0.02 | 0.02 |
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