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 |
| ATP1B3 | ENSG00000069849 | 0.03 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.07 | 0.01 | 0.08 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.07 | 0.01 | 0.53 | 0.01 | 0.28 | 0.00 | 0.32 | 0.01 | 0.11 | 0.02 | 0.01 | 0.01 | 0.05 | 0.00 | 0.00 | 0.00 | 0.06 | 0.01 | 0.00 | 0.03 | 0.09 | 0.01 | 0.00 | 0.05 | 0.00 | 0.00 | 0.10 | 0.02 | 0.53 | 0.03 | 0.31 | 0.01 | 0.11 | 0.00 | 0.26 | 0.02 | 0.13 | 0.07 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.02 | 0.00 | 0.01 | 0.03 | 0.04 | 0.00 | 0.00 | 0.01 | 0.05 |
| PMPCB | ENSG00000105819 | 0.01 | 0.00 | 0.07 | 0.00 | 0.01 | 0.00 | 0.04 | 0.01 | 0.05 | 0.02 | 0.00 | 0.00 | 0.03 | 0.00 | 0.09 | 0.02 | 0.18 | 0.02 | 0.20 | 0.01 | 0.44 | 0.04 | 0.18 | 0.03 | 0.02 | 0.01 | 0.01 | 0.01 | 0.02 | 0.02 | 0.06 | 0.02 | 0.00 | 0.02 | 0.02 | 0.06 | 0.00 | 0.01 | 0.00 | 0.00 | 0.05 | 0.04 | 0.25 | 0.06 | 0.04 | 0.02 | 0.05 | 0.03 | 0.09 | 0.07 | 0.08 | 0.04 | 0.08 | 0.01 | 0.00 | 0.00 | 0.13 | 0.00 | 0.07 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.06 | 0.04 |
| STK25 | ENSG00000115694 | 0.01 | 0.08 | 0.04 | 0.05 | 0.00 | 0.10 | 0.02 | 0.04 | 0.00 | 0.33 | 0.00 | 0.01 | 0.00 | 0.07 | 0.05 | 0.05 | 0.03 | 0.20 | 0.02 | 0.19 | 0.05 | 0.19 | 0.03 | 0.11 | 0.02 | 0.03 | 0.04 | 0.04 | 0.04 | 0.04 | 0.03 | 0.10 | 0.05 | 0.01 | 0.05 | 0.11 | 0.00 | 0.01 | 0.00 | 0.01 | 0.03 | 0.12 | 0.22 | 0.30 | 0.02 | 0.38 | 0.03 | 0.08 | 0.13 | 0.09 | 0.05 | 0.54 | 0.03 | 0.07 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.15 | 0.00 | 0.04 | 0.04 | 0.05 | 0.01 | 0.15 |
| COL3A1 | ENSG00000168542 | 0.02 | 0.02 | 0.09 | 0.00 | 0.00 | 0.01 | 0.02 | 0.03 | 0.07 | 0.06 | 0.00 | 0.00 | 0.00 | 0.02 | 0.05 | 0.01 | 0.13 | 0.04 | 0.14 | 0.04 | 0.12 | 0.02 | 0.06 | 0.05 | 0.01 | 0.01 | 0.02 | 0.03 | 0.03 | 0.01 | 0.07 | 0.02 | 0.00 | 0.05 | 0.02 | 0.00 | 0.00 | 0.03 | 0.00 | 0.00 | 0.07 | 0.02 | 0.40 | 0.05 | 0.11 | 0.02 | 0.06 | 0.01 | 0.00 | 0.03 | 0.04 | 0.08 | 0.06 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.01 | 0.00 | 0.01 | 0.03 | 0.00 | 0.02 | 0.02 |
| F2 | ENSG00000180210 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.00 | 0.00 | 0.08 | 0.04 | 0.04 | 0.00 | 0.00 | 0.00 | 0.01 | 0.04 | 0.02 | 0.12 | 0.03 | 0.09 | 0.01 | 0.12 | 0.04 | 0.08 | 0.01 | 0.01 | 0.00 | 0.02 | 0.00 | 0.03 | 0.01 | 0.02 | 0.01 | 0.00 | 0.07 | 0.08 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.07 | 0.02 | 0.14 | 0.06 | 0.07 | 0.02 | 0.09 | 0.01 | 0.06 | 0.09 | 0.08 | 0.07 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.04 | 0.00 | 0.02 | 0.02 | 0.04 |
| SEMA3A | ENSG00000075213 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.02 | 0.04 | 0.01 | 0.00 | 0.00 | 0.03 | 0.02 | 0.06 | 0.02 | 0.19 | 0.02 | 0.12 | 0.01 | 0.20 | 0.03 | 0.15 | 0.01 | 0.02 | 0.01 | 0.01 | 0.00 | 0.03 | 0.00 | 0.04 | 0.01 | 0.04 | 0.01 | 0.06 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.06 | 0.03 | 0.17 | 0.07 | 0.04 | 0.01 | 0.03 | 0.02 | 0.12 | 0.03 | 0.11 | 0.06 | 0.10 | 0.00 | 0.00 | 0.00 | 0.10 | 0.00 | 0.02 | 0.00 | 0.06 | 0.01 | 0.00 | 0.00 | 0.04 | 0.02 |
| CPT1B | ENSG00000205560 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.03 | 0.01 | 0.03 | 0.01 | 0.12 | 0.00 | 0.03 | 0.00 | 0.06 | 0.02 | 0.12 | 0.06 | 0.09 | 0.02 | 0.04 | 0.03 | 0.03 | 0.03 | 0.07 | 0.00 | 0.04 | 0.01 | 0.09 | 0.01 | 0.10 | 0.07 | 0.07 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.06 | 0.00 | 0.01 | 0.06 | 0.06 | 0.02 | 0.64 | 0.03 | 0.07 | 0.03 | 0.15 | 0.06 | 0.27 | 0.06 | 0.15 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.09 | 0.00 | 0.05 | 0.00 | 0.10 | 0.00 | 0.00 | 0.12 | 0.05 |
| PRDM16 | ENSG00000142611 | 0.00 | 0.05 | 0.01 | 0.10 | 0.00 | 0.00 | 0.02 | 0.03 | 0.10 | 0.08 | 0.00 | 0.02 | 0.04 | 0.27 | 0.09 | 0.06 | 0.08 | 0.11 | 0.06 | 0.09 | 0.14 | 0.08 | 0.09 | 0.09 | 0.02 | 0.11 | 0.00 | 0.17 | 0.05 | 0.05 | 0.02 | 0.31 | 0.00 | 1.01 | 0.05 | 0.17 | 0.01 | 0.13 | 0.00 | 0.00 | 0.04 | 0.19 | 0.23 | 0.38 | 0.06 | 0.11 | 0.05 | 0.12 | 0.08 | 0.27 | 0.18 | 0.28 | 0.10 | 0.12 | 0.02 | 0.00 | 0.00 | 0.19 | 0.00 | 0.03 | 0.05 | 0.16 | 0.00 | 0.14 | 0.07 | 0.13 |
| FMO5 | ENSG00000131781 | 0.03 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.04 | 0.03 | 0.50 | 0.04 | 0.02 | 0.00 | 0.10 | 0.13 | 0.38 | 0.12 | 0.28 | 0.13 | 0.10 | 0.16 | 0.23 | 0.11 | 0.19 | 0.04 | 0.02 | 0.04 | 0.15 | 0.03 | 0.05 | 0.01 | 0.33 | 0.03 | 0.39 | 0.01 | 0.17 | 0.03 | 0.10 | 0.26 | 0.00 | 0.00 | 0.36 | 0.05 | 0.60 | 0.09 | 0.15 | 0.06 | 0.25 | 0.02 | 0.41 | 0.04 | 0.41 | 0.12 | 0.12 | 0.03 | 0.00 | 0.00 | 0.28 | 0.02 | 0.01 | 0.01 | 0.02 | 0.03 | 0.00 | 0.03 | 0.17 | 0.05 |
| LY9 | ENSG00000122224 | 0.03 | 0.00 | 0.01 | 0.01 | 0.00 | 0.03 | 0.02 | 0.05 | 0.88 | 0.00 | 0.02 | 0.00 | 0.10 | 0.02 | 0.27 | 0.00 | 0.29 | 0.00 | 0.06 | 0.00 | 0.29 | 0.00 | 0.14 | 0.00 | 0.03 | 0.00 | 0.11 | 0.00 | 0.06 | 0.00 | 0.30 | 0.00 | 0.30 | 0.01 | 0.16 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.33 | 0.00 | 0.37 | 0.02 | 0.17 | 0.00 | 0.14 | 0.00 | 0.41 | 0.00 | 0.44 | 0.02 | 0.10 | 0.00 | 0.00 | 0.00 | 0.25 | 0.00 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.17 | 0.01 |
| DKK3 | ENSG00000050165 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.01 | 0.02 | 0.08 | 0.00 | 0.00 | 0.02 | 0.01 | 0.06 | 0.04 | 0.09 | 0.10 | 0.02 | 0.05 | 0.06 | 0.07 | 0.05 | 0.03 | 0.02 | 0.00 | 0.02 | 0.01 | 0.01 | 0.03 | 0.04 | 0.01 | 0.00 | 0.03 | 0.01 | 0.04 | 0.02 | 0.05 | 0.00 | 0.00 | 0.05 | 0.08 | 0.06 | 0.34 | 0.02 | 0.04 | 0.05 | 0.05 | 0.05 | 0.05 | 0.04 | 0.11 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.07 | 0.01 | 0.03 | 0.00 | 0.00 | 0.03 | 0.02 |
| P2RY13 | ENSG00000181631 | 0.03 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.05 | 0.01 | 0.13 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.10 | 0.02 | 0.86 | 0.01 | 0.44 | 0.00 | 0.53 | 0.02 | 0.11 | 0.00 | 0.01 | 0.00 | 0.05 | 0.01 | 0.02 | 0.00 | 0.08 | 0.01 | 0.03 | 0.03 | 0.09 | 0.01 | 0.00 | 0.05 | 0.00 | 0.00 | 0.16 | 0.01 | 0.69 | 0.02 | 0.41 | 0.00 | 0.14 | 0.01 | 0.23 | 0.07 | 0.05 | 0.09 | 0.08 | 0.00 | 0.00 | 0.00 | 0.01 | 0.08 | 0.00 | 0.01 | 0.02 | 0.03 | 0.00 | 0.00 | 0.03 | 0.04 |
| MBOAT7 | ENSG00000125505 | 0.01 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.03 | 0.00 | 0.17 | 0.02 | 0.00 | 0.00 | 0.01 | 0.05 | 0.02 | 0.06 | 0.10 | 0.09 | 0.04 | 0.02 | 0.09 | 0.03 | 0.10 | 0.03 | 0.02 | 0.03 | 0.01 | 0.04 | 0.03 | 0.04 | 0.07 | 0.02 | 0.00 | 0.07 | 0.25 | 0.00 | 0.00 | 0.03 | 0.00 | 0.00 | 0.16 | 0.03 | 0.14 | 0.26 | 0.14 | 0.06 | 0.06 | 0.06 | 0.35 | 0.11 | 0.11 | 0.16 | 0.00 | 0.06 | 0.01 | 0.00 | 0.13 | 0.03 | 0.00 | 0.17 | 0.02 | 0.11 | 0.00 | 0.00 | 0.04 | 0.03 |
| ADAMTS5 | ENSG00000154736 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.04 | 0.06 | 0.01 | 0.01 | 0.00 | 0.00 | 0.03 | 0.06 | 0.05 | 0.08 | 0.04 | 0.01 | 0.03 | 0.02 | 0.07 | 0.01 | 0.05 | 0.01 | 0.02 | 0.00 | 0.10 | 0.00 | 0.01 | 0.00 | 0.02 | 0.00 | 0.03 | 0.13 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.04 | 0.05 | 0.07 | 0.09 | 0.04 | 0.03 | 0.00 | 0.01 | 0.04 | 0.03 | 0.13 | 0.05 | 0.00 | 0.00 | 0.06 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.03 | 0.05 | 0.00 | 0.02 | 0.02 |
| JMJD6 | ENSG00000070495 | 0.02 | 0.00 | 0.05 | 0.00 | 0.02 | 0.00 | 0.04 | 0.03 | 0.19 | 0.00 | 0.00 | 0.01 | 0.09 | 0.02 | 0.16 | 0.01 | 0.21 | 0.02 | 0.08 | 0.04 | 0.20 | 0.07 | 0.09 | 0.03 | 0.04 | 0.01 | 0.06 | 0.03 | 0.04 | 0.10 | 0.26 | 0.02 | 0.08 | 0.01 | 0.08 | 0.02 | 0.02 | 0.01 | 0.00 | 0.00 | 0.35 | 0.03 | 0.34 | 0.04 | 0.17 | 0.05 | 0.14 | 0.02 | 0.45 | 0.04 | 0.19 | 0.03 | 0.05 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.07 | 0.00 | 0.04 | 0.01 | 0.12 | 0.04 | 0.25 | 0.02 |
| PRSS23 | ENSG00000150687 | 0.01 | 0.01 | 0.00 | 0.03 | 0.00 | 0.03 | 0.03 | 0.01 | 0.12 | 0.04 | 0.00 | 0.00 | 0.09 | 0.04 | 0.12 | 0.02 | 0.10 | 0.04 | 0.11 | 0.08 | 0.20 | 0.05 | 0.10 | 0.03 | 0.02 | 0.01 | 0.02 | 0.01 | 0.00 | 0.01 | 0.03 | 0.04 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.00 | 0.16 | 0.08 | 0.49 | 0.06 | 0.16 | 0.07 | 0.08 | 0.03 | 0.06 | 0.19 | 0.07 | 0.09 | 0.04 | 0.06 | 0.00 | 0.00 | 0.00 | 0.05 | 0.01 | 0.01 | 0.02 | 0.01 | 0.00 | 0.00 | 0.11 | 0.07 |
| TSHR | ENSG00000165409 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.03 | 0.01 | 0.04 | 0.04 | 0.04 | 0.00 | 0.00 | 0.00 | 0.05 | 0.02 | 0.05 | 0.07 | 0.03 | 0.03 | 0.03 | 0.05 | 0.05 | 0.02 | 0.04 | 0.01 | 0.03 | 0.01 | 0.05 | 0.01 | 0.01 | 0.01 | 0.08 | 0.00 | 0.31 | 0.01 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.02 | 0.09 | 0.17 | 0.18 | 0.05 | 0.05 | 0.03 | 0.02 | 0.13 | 0.08 | 0.07 | 0.11 | 0.03 | 0.01 | 0.00 | 0.00 | 0.04 | 0.00 | 0.00 | 0.11 | 0.01 | 0.07 | 0.03 | 0.00 | 0.02 | 0.06 |
| EDIL3 | ENSG00000164176 | 0.01 | 0.01 | 0.01 | 0.01 | 0.05 | 0.02 | 0.01 | 0.11 | 0.01 | 0.09 | 0.00 | 0.01 | 0.00 | 0.03 | 0.02 | 0.07 | 0.01 | 0.09 | 0.02 | 0.08 | 0.01 | 0.14 | 0.00 | 0.14 | 0.00 | 0.07 | 0.01 | 0.02 | 0.00 | 0.07 | 0.03 | 0.04 | 0.00 | 0.08 | 0.08 | 0.03 | 0.00 | 0.05 | 0.00 | 0.00 | 0.01 | 0.08 | 0.04 | 0.65 | 0.00 | 0.07 | 0.00 | 0.08 | 0.00 | 0.24 | 0.02 | 0.05 | 0.00 | 0.00 | 0.00 | 0.05 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.08 | 0.03 |
| SEMA4B | ENSG00000185033 | 0.02 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.02 | 0.02 | 0.04 | 0.03 | 0.03 | 0.00 | 0.06 | 0.00 | 0.08 | 0.01 | 0.24 | 0.01 | 0.06 | 0.02 | 0.28 | 0.01 | 0.35 | 0.01 | 0.05 | 0.01 | 0.11 | 0.00 | 0.08 | 0.00 | 0.07 | 0.05 | 0.05 | 0.01 | 0.05 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.19 | 0.02 | 0.33 | 0.08 | 0.19 | 0.01 | 0.07 | 0.02 | 0.36 | 0.01 | 0.12 | 0.04 | 0.00 | 0.01 | 0.00 | 0.00 | 0.06 | 0.00 | 0.01 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.19 | 0.02 |
| SLC27A2 | ENSG00000140284 | 0.00 | 0.00 | 0.00 | 0.01 | 0.14 | 0.00 | 0.01 | 0.04 | 0.05 | 0.04 | 0.00 | 0.00 | 0.07 | 0.11 | 0.01 | 0.05 | 0.03 | 0.05 | 0.03 | 0.02 | 0.03 | 0.03 | 0.01 | 0.07 | 0.01 | 0.03 | 0.00 | 0.05 | 0.00 | 0.02 | 0.01 | 0.03 | 0.00 | 0.01 | 0.02 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.07 | 0.09 | 0.06 | 0.22 | 0.01 | 0.10 | 0.00 | 0.07 | 0.08 | 0.26 | 0.13 | 0.05 | 0.01 | 0.03 | 0.00 | 0.00 | 0.06 | 0.05 | 0.00 | 0.02 | 0.00 | 0.09 | 0.00 | 0.00 | 0.04 | 0.11 |
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