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 |
| ECE1 | ENSG00000117298 | 0.00 | 0.05 | 0.00 | 0.08 | 0.00 | 0.00 | 0.01 | 0.03 | 0.08 | 0.09 | 0.00 | 0.01 | 0.04 | 0.25 | 0.05 | 0.06 | 0.03 | 0.11 | 0.03 | 0.07 | 0.03 | 0.10 | 0.06 | 0.12 | 0.00 | 0.16 | 0.00 | 0.21 | 0.01 | 0.09 | 0.02 | 0.22 | 0.00 | 1.11 | 0.09 | 0.05 | 0.01 | 0.10 | 0.00 | 0.00 | 0.02 | 0.19 | 0.12 | 0.45 | 0.04 | 0.09 | 0.06 | 0.13 | 0.18 | 0.21 | 0.17 | 0.12 | 0.05 | 0.06 | 0.02 | 0.00 | 0.00 | 0.07 | 0.00 | 0.03 | 0.04 | 0.10 | 0.00 | 0.12 | 0.05 | 0.09 |
| SERPINF2 | ENSG00000167711 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.06 | 0.05 | 0.05 | 0.00 | 0.00 | 0.01 | 0.02 | 0.01 | 0.07 | 0.03 | 0.03 | 0.01 | 0.03 | 0.06 | 0.06 | 0.03 | 0.03 | 0.04 | 0.02 | 0.01 | 0.00 | 0.00 | 0.03 | 0.04 | 0.13 | 0.01 | 0.03 | 0.07 | 0.03 | 0.00 | 0.04 | 0.00 | 0.00 | 0.02 | 0.06 | 0.15 | 0.11 | 0.02 | 0.03 | 0.07 | 0.05 | 0.16 | 0.12 | 0.18 | 0.22 | 0.01 | 0.02 | 0.00 | 0.02 | 0.00 | 0.06 | 0.01 | 0.00 | 0.01 | 0.04 | 0.00 | 0.00 | 0.02 | 0.05 |
| TSPAN7 | ENSG00000156298 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.05 | 0.03 | 0.06 | 0.02 | 0.00 | 0.00 | 0.00 | 0.02 | 0.04 | 0.04 | 0.03 | 0.02 | 0.02 | 0.03 | 0.11 | 0.05 | 0.03 | 0.01 | 0.00 | 0.01 | 0.02 | 0.00 | 0.00 | 0.01 | 0.00 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.02 | 0.02 | 0.08 | 0.13 | 0.00 | 0.01 | 0.04 | 0.02 | 0.13 | 0.07 | 0.15 | 0.03 | 0.01 | 0.00 | 0.00 | 0.01 | 0.06 | 0.04 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 |
| SEMA4D | ENSG00000187764 | 0.01 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.02 | 0.02 | 0.05 | 0.04 | 0.00 | 0.02 | 0.01 | 0.05 | 0.01 | 0.03 | 0.04 | 0.02 | 0.03 | 0.00 | 0.07 | 0.02 | 0.03 | 0.04 | 0.03 | 0.01 | 0.04 | 0.02 | 0.00 | 0.00 | 0.02 | 0.02 | 0.00 | 0.08 | 0.04 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.03 | 0.03 | 0.06 | 0.14 | 0.00 | 0.02 | 0.05 | 0.03 | 0.07 | 0.15 | 0.15 | 0.01 | 0.04 | 0.02 | 0.00 | 0.02 | 0.05 | 0.02 | 0.00 | 0.00 | 0.01 | 0.02 | 0.00 | 0.00 | 0.00 | 0.02 |
| TRPM2 | ENSG00000142185 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.03 | 0.05 | 0.04 | 0.00 | 0.02 | 0.00 | 0.01 | 0.03 | 0.03 | 0.03 | 0.06 | 0.02 | 0.06 | 0.06 | 0.08 | 0.02 | 0.06 | 0.02 | 0.03 | 0.01 | 0.05 | 0.01 | 0.01 | 0.03 | 0.02 | 0.05 | 0.07 | 0.09 | 0.04 | 0.01 | 0.00 | 0.00 | 0.00 | 0.10 | 0.02 | 0.21 | 0.18 | 0.05 | 0.03 | 0.06 | 0.02 | 0.10 | 0.08 | 0.08 | 0.09 | 0.04 | 0.00 | 0.10 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.02 | 0.06 | 0.00 | 0.02 | 0.03 |
| RPS6KA4 | ENSG00000162302 | 0.01 | 0.00 | 0.00 | 0.01 | 0.07 | 0.00 | 0.03 | 0.01 | 0.12 | 0.01 | 0.00 | 0.00 | 0.08 | 0.00 | 0.05 | 0.03 | 0.08 | 0.02 | 0.19 | 0.03 | 0.12 | 0.05 | 0.02 | 0.02 | 0.01 | 0.01 | 0.02 | 0.03 | 0.00 | 0.02 | 0.01 | 0.03 | 0.13 | 0.07 | 0.07 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.09 | 0.08 | 0.16 | 0.04 | 0.08 | 0.01 | 0.09 | 0.03 | 0.50 | 0.04 | 0.07 | 0.03 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.08 | 0.04 |
| ABCA8 | ENSG00000141338 | 0.02 | 0.00 | 0.04 | 0.01 | 0.00 | 0.00 | 0.03 | 0.03 | 0.22 | 0.01 | 0.05 | 0.00 | 0.12 | 0.00 | 0.16 | 0.00 | 0.21 | 0.01 | 0.07 | 0.02 | 0.24 | 0.04 | 0.13 | 0.03 | 0.05 | 0.01 | 0.06 | 0.03 | 0.05 | 0.10 | 0.23 | 0.01 | 0.12 | 0.01 | 0.15 | 0.12 | 0.02 | 0.01 | 0.00 | 0.00 | 0.45 | 0.02 | 0.26 | 0.03 | 0.18 | 0.02 | 0.11 | 0.01 | 0.34 | 0.02 | 0.25 | 0.04 | 0.03 | 0.00 | 0.00 | 0.00 | 0.05 | 0.00 | 0.07 | 0.00 | 0.02 | 0.01 | 0.17 | 0.01 | 0.22 | 0.01 |
| SLC37A1 | ENSG00000160190 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.04 | 0.05 | 0.05 | 0.00 | 0.03 | 0.00 | 0.00 | 0.03 | 0.02 | 0.02 | 0.07 | 0.01 | 0.05 | 0.04 | 0.08 | 0.04 | 0.07 | 0.01 | 0.01 | 0.02 | 0.05 | 0.01 | 0.01 | 0.02 | 0.02 | 0.05 | 0.07 | 0.01 | 0.04 | 0.01 | 0.00 | 0.00 | 0.00 | 0.09 | 0.02 | 0.15 | 0.17 | 0.03 | 0.03 | 0.04 | 0.02 | 0.14 | 0.03 | 0.06 | 0.08 | 0.04 | 0.00 | 0.12 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.03 | 0.00 | 0.01 | 0.03 |
| FBLN1 | ENSG00000077942 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.05 | 0.03 | 0.10 | 0.00 | 0.02 | 0.00 | 0.04 | 0.04 | 0.09 | 0.05 | 0.06 | 0.03 | 0.03 | 0.03 | 0.04 | 0.02 | 0.06 | 0.00 | 0.03 | 0.01 | 0.11 | 0.01 | 0.08 | 0.04 | 0.06 | 0.00 | 0.05 | 0.00 | 0.00 | 0.00 | 0.06 | 0.00 | 0.00 | 0.05 | 0.05 | 0.04 | 0.48 | 0.05 | 0.05 | 0.03 | 0.10 | 0.09 | 0.36 | 0.04 | 0.12 | 0.00 | 0.04 | 0.01 | 0.00 | 0.03 | 0.09 | 0.00 | 0.04 | 0.00 | 0.09 | 0.00 | 0.00 | 0.15 | 0.04 |
| LDLR | ENSG00000130164 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.02 | 0.08 | 0.04 | 0.00 | 0.01 | 0.09 | 0.01 | 0.01 | 0.06 | 0.07 | 0.06 | 0.05 | 0.04 | 0.11 | 0.06 | 0.05 | 0.03 | 0.02 | 0.01 | 0.02 | 0.02 | 0.01 | 0.03 | 0.05 | 0.10 | 0.00 | 0.01 | 0.14 | 0.02 | 0.00 | 0.00 | 0.00 | 0.01 | 0.09 | 0.04 | 0.56 | 0.20 | 0.11 | 0.04 | 0.26 | 0.04 | 0.55 | 0.13 | 0.30 | 0.02 | 0.02 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.05 | 0.00 | 0.02 | 0.02 | 0.02 | 0.02 |
| KCNG1 | ENSG00000026559 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.00 | 0.14 | 0.02 | 0.00 | 0.00 | 0.03 | 0.00 | 0.10 | 0.03 | 0.13 | 0.01 | 0.01 | 0.01 | 0.11 | 0.01 | 0.20 | 0.00 | 0.11 | 0.00 | 0.08 | 0.00 | 0.01 | 0.01 | 0.08 | 0.01 | 0.00 | 0.01 | 0.04 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.32 | 0.01 | 0.32 | 0.02 | 0.02 | 0.03 | 0.08 | 0.01 | 0.24 | 0.00 | 0.15 | 0.03 | 0.02 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.12 | 0.00 |
| HSP90B1 | ENSG00000166598 | 0.01 | 0.01 | 0.02 | 0.00 | 0.06 | 0.02 | 0.04 | 0.03 | 0.06 | 0.03 | 0.00 | 0.00 | 0.04 | 0.02 | 0.02 | 0.05 | 0.02 | 0.04 | 0.01 | 0.03 | 0.04 | 0.05 | 0.05 | 0.03 | 0.00 | 0.01 | 0.01 | 0.03 | 0.00 | 0.06 | 0.03 | 0.04 | 0.00 | 0.22 | 0.00 | 0.02 | 0.00 | 0.03 | 0.00 | 0.00 | 0.03 | 0.08 | 0.06 | 0.21 | 0.01 | 0.01 | 0.02 | 0.04 | 0.02 | 0.11 | 0.23 | 0.04 | 0.00 | 0.01 | 0.00 | 0.00 | 0.08 | 0.02 | 0.01 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.08 |
| KDM1A | ENSG00000004487 | 0.00 | 0.06 | 0.00 | 0.08 | 0.00 | 0.00 | 0.01 | 0.04 | 0.07 | 0.09 | 0.00 | 0.03 | 0.04 | 0.23 | 0.04 | 0.06 | 0.05 | 0.11 | 0.03 | 0.07 | 0.03 | 0.10 | 0.05 | 0.11 | 0.00 | 0.16 | 0.00 | 0.21 | 0.01 | 0.08 | 0.01 | 0.22 | 0.00 | 1.06 | 0.05 | 0.06 | 0.01 | 0.10 | 0.00 | 0.00 | 0.01 | 0.19 | 0.12 | 0.45 | 0.04 | 0.08 | 0.04 | 0.13 | 0.09 | 0.19 | 0.16 | 0.11 | 0.05 | 0.06 | 0.02 | 0.00 | 0.00 | 0.15 | 0.04 | 0.03 | 0.04 | 0.10 | 0.00 | 0.12 | 0.07 | 0.09 |
| MSR1 | ENSG00000038945 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.18 | 0.01 | 0.14 | 0.00 | 0.00 | 0.02 | 0.05 | 0.02 | 0.07 | 0.02 | 0.09 | 0.01 | 0.08 | 0.10 | 0.05 | 0.09 | 0.04 | 0.01 | 0.13 | 0.00 | 0.19 | 0.01 | 0.05 | 0.02 | 0.12 | 0.00 | 0.05 | 0.02 | 0.02 | 0.00 | 0.05 | 0.00 | 0.00 | 0.03 | 0.14 | 0.03 | 0.43 | 0.01 | 0.05 | 0.00 | 0.09 | 0.07 | 0.21 | 0.10 | 0.05 | 0.04 | 0.01 | 0.00 | 0.00 | 0.00 | 0.09 | 0.00 | 0.02 | 0.00 | 0.03 | 0.02 | 0.01 | 0.01 | 0.04 |
| ADGRG5 | ENSG00000159618 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.01 | 0.04 | 0.00 | 0.00 | 0.00 | 0.01 | 0.04 | 0.03 | 0.04 | 0.01 | 0.03 | 0.02 | 0.10 | 0.01 | 0.03 | 0.04 | 0.02 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.01 | 0.03 | 0.00 | 0.01 | 0.06 | 0.06 | 0.00 | 0.02 | 0.00 | 0.00 | 0.04 | 0.04 | 0.05 | 0.14 | 0.00 | 0.07 | 0.04 | 0.07 | 0.03 | 0.16 | 0.02 | 0.05 | 0.12 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.01 | 0.01 | 0.02 | 0.00 | 0.03 | 0.02 | 0.03 |
| PLCD4 | ENSG00000115556 | 0.02 | 0.06 | 0.04 | 0.04 | 0.00 | 0.03 | 0.01 | 0.02 | 0.01 | 0.27 | 0.00 | 0.01 | 0.00 | 0.10 | 0.02 | 0.03 | 0.04 | 0.19 | 0.01 | 0.18 | 0.03 | 0.11 | 0.06 | 0.03 | 0.02 | 0.01 | 0.03 | 0.02 | 0.05 | 0.03 | 0.03 | 0.04 | 0.00 | 0.01 | 0.04 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.04 | 0.06 | 0.18 | 0.16 | 0.04 | 0.34 | 0.06 | 0.04 | 0.22 | 0.05 | 0.08 | 0.21 | 0.08 | 0.01 | 0.00 | 0.00 | 0.00 | 0.04 | 0.01 | 0.02 | 0.01 | 0.00 | 0.02 | 0.02 | 0.03 | 0.03 |
| TET2 | ENSG00000168769 | 0.00 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.05 | 0.03 | 0.05 | 0.00 | 0.00 | 0.00 | 0.06 | 0.02 | 0.03 | 0.03 | 0.05 | 0.02 | 0.02 | 0.02 | 0.06 | 0.02 | 0.05 | 0.01 | 0.02 | 0.00 | 0.04 | 0.01 | 0.01 | 0.01 | 0.13 | 0.00 | 0.11 | 0.04 | 0.04 | 0.04 | 0.01 | 0.00 | 0.00 | 0.04 | 0.05 | 0.02 | 0.30 | 0.01 | 0.02 | 0.01 | 0.05 | 0.00 | 0.11 | 0.04 | 0.06 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.02 | 0.01 | 0.03 | 0.00 | 0.03 | 0.00 | 0.00 | 0.02 | 0.05 |
| HMCN1 | ENSG00000143341 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.03 | 0.22 | 0.04 | 0.02 | 0.00 | 0.10 | 0.03 | 0.10 | 0.00 | 0.15 | 0.01 | 0.05 | 0.01 | 0.19 | 0.03 | 0.08 | 0.00 | 0.03 | 0.01 | 0.15 | 0.01 | 0.05 | 0.00 | 0.18 | 0.02 | 0.20 | 0.01 | 0.00 | 0.05 | 0.01 | 0.00 | 0.01 | 0.00 | 0.18 | 0.01 | 0.35 | 0.04 | 0.10 | 0.00 | 0.07 | 0.00 | 0.20 | 0.00 | 0.26 | 0.06 | 0.07 | 0.00 | 0.01 | 0.00 | 0.30 | 0.02 | 0.01 | 0.01 | 0.01 | 0.01 | 0.04 | 0.00 | 0.13 | 0.04 |
| CACNA2D2 | ENSG00000007402 | 0.00 | 0.18 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.02 | 0.03 | 0.17 | 0.02 | 0.00 | 0.00 | 0.54 | 0.01 | 0.06 | 0.00 | 0.11 | 0.00 | 0.06 | 0.03 | 0.14 | 0.01 | 0.11 | 0.00 | 0.05 | 0.01 | 0.07 | 0.00 | 0.05 | 0.04 | 0.06 | 0.00 | 0.20 | 0.01 | 0.02 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.17 | 0.05 | 0.20 | 0.00 | 0.06 | 0.08 | 0.07 | 0.15 | 0.36 | 0.03 | 0.16 | 0.02 | 0.02 | 0.00 | 0.01 | 0.00 | 0.06 | 0.01 | 0.06 | 0.01 | 0.04 | 0.00 | 0.03 | 0.02 | 0.05 |
| NAALADL2 | ENSG00000177694 | 0.06 | 0.00 | 0.03 | 0.01 | 0.02 | 0.03 | 0.08 | 0.02 | 0.18 | 0.03 | 0.00 | 0.00 | 0.00 | 0.07 | 0.17 | 0.04 | 1.77 | 0.01 | 0.65 | 0.02 | 0.79 | 0.19 | 0.28 | 0.21 | 0.04 | 0.17 | 0.06 | 0.19 | 0.03 | 0.00 | 0.14 | 0.06 | 0.12 | 0.01 | 0.10 | 0.11 | 0.00 | 0.08 | 0.00 | 0.00 | 0.25 | 0.02 | 1.27 | 0.02 | 0.72 | 0.03 | 0.37 | 0.01 | 0.97 | 0.17 | 0.09 | 0.12 | 0.20 | 0.01 | 0.00 | 0.00 | 0.06 | 0.00 | 0.03 | 0.01 | 0.10 | 0.03 | 0.00 | 0.00 | 0.02 | 0.07 |
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