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 |
| ATP8B1 | ENSG00000081923 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.08 | 0.01 | 0.08 | 0.00 | 0.00 | 0.00 | 0.02 | 0.02 | 0.11 | 0.03 | 0.07 | 0.01 | 0.13 | 0.04 | 0.20 | 0.01 | 0.19 | 0.00 | 0.10 | 0.00 | 0.09 | 0.00 | 0.08 | 0.02 | 0.07 | 0.05 | 0.10 | 0.01 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.06 | 0.05 | 0.32 | 0.02 | 0.04 | 0.02 | 0.06 | 0.01 | 0.09 | 0.12 | 0.07 | 0.00 | 0.05 | 0.00 | 0.01 | 0.12 | 0.00 | 0.01 | 0.03 | 0.00 | 0.03 | 0.00 | 0.01 | 0.02 | 0.02 |
| IL12RB2 | ENSG00000081985 | 0.00 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.06 | 0.05 | 0.05 | 0.00 | 0.02 | 0.02 | 0.03 | 0.06 | 0.05 | 0.03 | 0.05 | 0.02 | 0.04 | 0.02 | 0.06 | 0.03 | 0.04 | 0.00 | 0.07 | 0.00 | 0.07 | 0.00 | 0.01 | 0.04 | 0.03 | 0.00 | 0.12 | 0.02 | 0.03 | 0.00 | 0.17 | 0.00 | 0.00 | 0.06 | 0.06 | 0.16 | 0.12 | 0.04 | 0.04 | 0.03 | 0.02 | 0.00 | 0.06 | 0.18 | 0.03 | 0.01 | 0.04 | 0.02 | 0.01 | 0.00 | 0.03 | 0.00 | 0.01 | 0.03 | 0.02 | 0.03 | 0.07 | 0.02 | 0.05 |
| STRADB | ENSG00000082146 | 0.03 | 0.02 | 0.04 | 0.02 | 0.00 | 0.01 | 0.01 | 0.02 | 0.02 | 0.14 | 0.00 | 0.02 | 0.00 | 0.05 | 0.04 | 0.02 | 0.15 | 0.09 | 0.09 | 0.11 | 0.12 | 0.07 | 0.05 | 0.04 | 0.02 | 0.01 | 0.03 | 0.00 | 0.07 | 0.01 | 0.06 | 0.01 | 0.00 | 0.01 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.04 | 0.26 | 0.08 | 0.09 | 0.18 | 0.04 | 0.02 | 0.06 | 0.05 | 0.07 | 0.11 | 0.06 | 0.00 | 0.00 | 0.01 | 0.00 | 0.04 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.02 | 0.02 | 0.03 |
| COL19A1 | ENSG00000082293 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.15 | 0.07 | 0.07 | 0.00 | 0.00 | 0.01 | 0.05 | 0.03 | 0.05 | 0.14 | 0.03 | 0.03 | 0.04 | 0.13 | 0.08 | 0.04 | 0.05 | 0.03 | 0.02 | 0.01 | 0.00 | 0.01 | 0.02 | 0.06 | 0.04 | 0.09 | 0.17 | 0.04 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.06 | 0.07 | 0.14 | 0.10 | 0.01 | 0.02 | 0.03 | 0.01 | 0.06 | 0.08 | 0.05 | 0.17 | 0.04 | 0.00 | 0.00 | 0.00 | 0.02 | 0.06 | 0.00 | 0.01 | 0.01 | 0.03 | 0.06 | 0.03 | 0.04 | 0.04 |
| OPRK1 | ENSG00000082556 | 0.00 | 0.00 | 0.00 | 0.00 | 0.11 | 0.00 | 0.04 | 0.02 | 0.11 | 0.02 | 0.00 | 0.00 | 0.00 | 0.07 | 0.10 | 0.02 | 0.13 | 0.03 | 0.05 | 0.01 | 0.08 | 0.03 | 0.08 | 0.02 | 0.05 | 0.02 | 0.11 | 0.01 | 0.01 | 0.01 | 0.02 | 0.02 | 0.00 | 0.02 | 0.03 | 0.00 | 0.01 | 0.02 | 0.00 | 0.00 | 0.15 | 0.03 | 0.38 | 0.02 | 0.02 | 0.01 | 0.12 | 0.01 | 0.79 | 0.09 | 0.10 | 0.04 | 0.16 | 0.00 | 0.01 | 0.00 | 0.04 | 0.03 | 0.00 | 0.00 | 0.01 | 0.01 | 0.20 | 0.00 | 0.10 | 0.02 |
| TRPM3 | ENSG00000083067 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.03 | 0.06 | 0.00 | 0.02 | 0.03 | 0.06 | 0.01 | 0.06 | 0.06 | 0.06 | 0.01 | 0.03 | 0.08 | 0.04 | 0.06 | 0.05 | 0.00 | 0.02 | 0.02 | 0.04 | 0.00 | 0.00 | 0.03 | 0.03 | 0.00 | 0.15 | 0.05 | 0.00 | 0.00 | 0.07 | 0.00 | 0.00 | 0.03 | 0.05 | 0.11 | 0.15 | 0.01 | 0.03 | 0.03 | 0.04 | 0.06 | 0.16 | 0.15 | 0.02 | 0.02 | 0.02 | 0.00 | 0.02 | 0.10 | 0.05 | 0.00 | 0.01 | 0.02 | 0.04 | 0.00 | 0.00 | 0.03 | 0.03 |
| P2RX5 | ENSG00000083454 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.06 | 0.05 | 0.03 | 0.00 | 0.00 | 0.01 | 0.02 | 0.01 | 0.06 | 0.02 | 0.02 | 0.01 | 0.03 | 0.04 | 0.04 | 0.03 | 0.02 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.03 | 0.01 | 0.12 | 0.02 | 0.03 | 0.02 | 0.03 | 0.00 | 0.03 | 0.00 | 0.00 | 0.03 | 0.05 | 0.14 | 0.09 | 0.01 | 0.03 | 0.04 | 0.04 | 0.06 | 0.13 | 0.15 | 0.23 | 0.00 | 0.02 | 0.00 | 0.02 | 0.00 | 0.06 | 0.00 | 0.00 | 0.00 | 0.05 | 0.00 | 0.00 | 0.03 | 0.03 |
| ITGAE | ENSG00000083457 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.07 | 0.05 | 0.03 | 0.00 | 0.00 | 0.01 | 0.02 | 0.01 | 0.06 | 0.02 | 0.02 | 0.01 | 0.03 | 0.04 | 0.04 | 0.03 | 0.02 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.03 | 0.01 | 0.12 | 0.02 | 0.03 | 0.02 | 0.03 | 0.00 | 0.03 | 0.00 | 0.00 | 0.03 | 0.05 | 0.14 | 0.08 | 0.01 | 0.03 | 0.04 | 0.05 | 0.07 | 0.13 | 0.16 | 0.23 | 0.00 | 0.02 | 0.00 | 0.03 | 0.00 | 0.06 | 0.00 | 0.00 | 0.00 | 0.05 | 0.00 | 0.00 | 0.04 | 0.04 |
| PPIE | ENSG00000084072 | 0.01 | 0.02 | 0.01 | 0.04 | 0.00 | 0.00 | 0.01 | 0.01 | 0.34 | 0.03 | 0.00 | 0.00 | 0.11 | 0.03 | 0.12 | 0.02 | 0.17 | 0.03 | 0.09 | 0.02 | 0.30 | 0.02 | 0.06 | 0.03 | 0.04 | 0.02 | 0.01 | 0.03 | 0.04 | 0.01 | 0.03 | 0.10 | 0.00 | 0.31 | 0.00 | 0.03 | 0.03 | 0.07 | 0.00 | 0.00 | 0.08 | 0.04 | 0.75 | 0.06 | 0.07 | 0.01 | 0.12 | 0.01 | 0.21 | 0.05 | 0.11 | 0.05 | 0.05 | 0.03 | 0.02 | 0.00 | 0.00 | 0.03 | 0.00 | 0.01 | 0.04 | 0.01 | 0.02 | 0.10 | 0.05 | 0.03 |
| SSH1 | ENSG00000084112 | 0.01 | 0.01 | 0.02 | 0.00 | 0.06 | 0.02 | 0.04 | 0.03 | 0.09 | 0.03 | 0.00 | 0.00 | 0.02 | 0.00 | 0.02 | 0.05 | 0.02 | 0.04 | 0.02 | 0.03 | 0.08 | 0.05 | 0.05 | 0.02 | 0.00 | 0.01 | 0.02 | 0.01 | 0.00 | 0.06 | 0.04 | 0.03 | 0.00 | 0.22 | 0.11 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.04 | 0.07 | 0.10 | 0.21 | 0.01 | 0.01 | 0.02 | 0.05 | 0.08 | 0.07 | 0.16 | 0.05 | 0.00 | 0.01 | 0.00 | 0.00 | 0.10 | 0.00 | 0.00 | 0.04 | 0.01 | 0.02 | 0.00 | 0.00 | 0.02 | 0.07 |
| GSTP1 | ENSG00000084207 | 0.01 | 0.00 | 0.03 | 0.01 | 0.09 | 0.02 | 0.10 | 0.00 | 0.25 | 0.01 | 0.00 | 0.00 | 0.08 | 0.00 | 0.15 | 0.01 | 0.18 | 0.02 | 0.42 | 0.02 | 0.50 | 0.02 | 0.17 | 0.03 | 0.01 | 0.01 | 0.05 | 0.02 | 0.03 | 0.01 | 0.14 | 0.01 | 0.19 | 0.01 | 0.05 | 0.03 | 0.03 | 0.00 | 0.00 | 0.00 | 0.49 | 0.04 | 0.27 | 0.03 | 0.22 | 0.01 | 0.15 | 0.02 | 0.19 | 0.04 | 0.13 | 0.03 | 0.00 | 0.05 | 0.00 | 0.00 | 0.00 | 0.06 | 0.01 | 0.01 | 0.00 | 0.04 | 0.00 | 0.00 | 0.25 | 0.02 |
| CAD | ENSG00000084774 | 0.00 | 0.00 | 0.04 | 0.01 | 0.00 | 0.00 | 0.01 | 0.01 | 0.09 | 0.01 | 0.00 | 0.00 | 0.03 | 0.07 | 0.06 | 0.01 | 0.10 | 0.01 | 0.03 | 0.01 | 0.05 | 0.05 | 0.04 | 0.03 | 0.01 | 0.00 | 0.02 | 0.02 | 0.01 | 0.04 | 0.11 | 0.00 | 0.00 | 0.05 | 0.06 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.03 | 0.22 | 0.07 | 0.08 | 0.00 | 0.12 | 0.02 | 0.25 | 0.00 | 0.04 | 0.08 | 0.17 | 0.01 | 0.00 | 0.00 | 0.02 | 0.02 | 0.00 | 0.00 | 0.01 | 0.02 | 0.05 | 0.00 | 0.03 | 0.03 |
| CD59 | ENSG00000085063 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.03 | 0.14 | 0.04 | 0.00 | 0.00 | 0.00 | 0.04 | 0.06 | 0.02 | 0.11 | 0.02 | 0.12 | 0.01 | 0.28 | 0.02 | 0.09 | 0.01 | 0.01 | 0.00 | 0.01 | 0.00 | 0.01 | 0.02 | 0.01 | 0.01 | 0.00 | 0.05 | 0.02 | 0.01 | 0.02 | 0.04 | 0.00 | 0.00 | 0.18 | 0.01 | 0.21 | 0.06 | 0.05 | 0.01 | 0.03 | 0.02 | 0.01 | 0.05 | 0.12 | 0.07 | 0.00 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.03 | 0.02 |
| FCN1 | ENSG00000085265 | 0.00 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.04 | 0.01 | 0.03 | 0.03 | 0.00 | 0.01 | 0.00 | 0.02 | 0.05 | 0.03 | 0.07 | 0.02 | 0.07 | 0.03 | 0.12 | 0.02 | 0.11 | 0.02 | 0.03 | 0.01 | 0.08 | 0.04 | 0.01 | 0.00 | 0.06 | 0.04 | 0.06 | 0.01 | 0.12 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.05 | 0.06 | 0.08 | 0.25 | 0.06 | 0.02 | 0.01 | 0.05 | 0.03 | 0.14 | 0.07 | 0.15 | 0.03 | 0.03 | 0.01 | 0.00 | 0.05 | 0.00 | 0.02 | 0.01 | 0.04 | 0.03 | 0.00 | 0.00 | 0.03 | 0.02 |
| OVGP1 | ENSG00000085465 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.05 | 0.05 | 0.05 | 0.00 | 0.00 | 0.00 | 0.35 | 0.01 | 0.14 | 0.01 | 0.15 | 0.00 | 0.13 | 0.03 | 0.13 | 0.02 | 0.07 | 0.00 | 0.06 | 0.05 | 0.08 | 0.00 | 0.02 | 0.01 | 0.03 | 0.00 | 0.10 | 0.06 | 0.04 | 0.00 | 0.25 | 0.00 | 0.00 | 0.03 | 0.10 | 0.18 | 0.14 | 0.01 | 0.08 | 0.01 | 0.03 | 0.01 | 0.07 | 0.03 | 0.11 | 0.04 | 0.04 | 0.00 | 0.01 | 0.00 | 0.08 | 0.00 | 0.01 | 0.01 | 0.03 | 0.03 | 0.03 | 0.07 | 0.10 |
| AKR1B1 | ENSG00000085662 | 0.01 | 0.01 | 0.10 | 0.00 | 0.04 | 0.00 | 0.03 | 0.03 | 0.06 | 0.04 | 0.00 | 0.01 | 0.04 | 0.05 | 0.06 | 0.02 | 0.06 | 0.06 | 0.03 | 0.14 | 0.04 | 0.21 | 0.04 | 0.07 | 0.03 | 0.00 | 0.03 | 0.01 | 0.02 | 0.04 | 0.04 | 0.04 | 0.00 | 0.02 | 0.03 | 0.06 | 0.00 | 0.01 | 0.00 | 0.01 | 0.08 | 0.03 | 0.45 | 0.03 | 0.03 | 0.08 | 0.06 | 0.05 | 0.05 | 0.16 | 0.18 | 0.03 | 0.02 | 0.03 | 0.00 | 0.05 | 0.02 | 0.17 | 0.11 | 0.00 | 0.07 | 0.01 | 0.00 | 0.03 | 0.21 | 0.02 |
| ORC1 | ENSG00000085840 | 0.00 | 0.01 | 0.02 | 0.02 | 0.00 | 0.00 | 0.00 | 0.06 | 0.08 | 0.04 | 0.00 | 0.00 | 0.06 | 0.04 | 0.07 | 0.04 | 0.05 | 0.03 | 0.04 | 0.03 | 0.03 | 0.03 | 0.02 | 0.04 | 0.01 | 0.04 | 0.02 | 0.03 | 0.01 | 0.01 | 0.02 | 0.06 | 0.00 | 0.25 | 0.02 | 0.03 | 0.00 | 0.16 | 0.00 | 0.00 | 0.06 | 0.04 | 0.29 | 0.10 | 0.08 | 0.02 | 0.04 | 0.02 | 0.04 | 0.04 | 0.25 | 0.02 | 0.07 | 0.04 | 0.02 | 0.00 | 0.00 | 0.03 | 0.00 | 0.01 | 0.01 | 0.03 | 0.00 | 0.07 | 0.04 | 0.03 |
| MGST2 | ENSG00000085871 | 0.01 | 0.02 | 0.00 | 0.01 | 0.06 | 0.00 | 0.02 | 0.02 | 0.05 | 0.08 | 0.00 | 0.00 | 0.00 | 0.03 | 0.02 | 0.04 | 0.02 | 0.09 | 0.03 | 0.05 | 0.07 | 0.03 | 0.09 | 0.04 | 0.01 | 0.02 | 0.02 | 0.02 | 0.00 | 0.02 | 0.07 | 0.06 | 0.00 | 0.03 | 0.08 | 0.07 | 0.00 | 0.01 | 0.00 | 0.00 | 0.04 | 0.04 | 0.10 | 0.16 | 0.03 | 0.05 | 0.03 | 0.03 | 0.07 | 0.04 | 0.09 | 0.09 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.08 | 0.01 | 0.02 | 0.00 | 0.00 | 0.06 | 0.03 |
| AQP6 | ENSG00000086159 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.06 | 0.03 | 0.00 | 0.00 | 0.00 | 0.04 | 0.06 | 0.02 | 0.03 | 0.02 | 0.01 | 0.03 | 0.06 | 0.03 | 0.05 | 0.04 | 0.02 | 0.00 | 0.02 | 0.01 | 0.01 | 0.05 | 0.01 | 0.01 | 0.00 | 0.01 | 0.19 | 0.00 | 0.01 | 0.02 | 0.00 | 0.00 | 0.03 | 0.06 | 0.10 | 0.06 | 0.03 | 0.01 | 0.05 | 0.01 | 0.33 | 0.06 | 0.05 | 0.09 | 0.02 | 0.00 | 0.00 | 0.01 | 0.10 | 0.03 | 0.00 | 0.04 | 0.04 | 0.05 | 0.00 | 0.00 | 0.06 | 0.06 |
| FOLH1 | ENSG00000086205 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.00 | 0.00 | 0.06 | 0.04 | 0.05 | 0.00 | 0.01 | 0.00 | 0.01 | 0.04 | 0.01 | 0.08 | 0.02 | 0.07 | 0.01 | 0.15 | 0.06 | 0.04 | 0.01 | 0.01 | 0.01 | 0.02 | 0.02 | 0.02 | 0.01 | 0.02 | 0.00 | 0.00 | 0.09 | 0.07 | 0.02 | 0.00 | 0.04 | 0.00 | 0.00 | 0.09 | 0.04 | 0.10 | 0.05 | 0.03 | 0.03 | 0.03 | 0.02 | 0.05 | 0.07 | 0.08 | 0.05 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.00 | 0.03 | 0.00 | 0.02 | 0.01 | 0.03 |
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