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 |
| SLC25A16 | ENSG00000122912 | 0.00 | 0.01 | 0.00 | 0.00 | 0.03 | 0.00 | 0.02 | 0.03 | 0.03 | 0.03 | 0.00 | 0.00 | 0.01 | 0.00 | 0.05 | 0.02 | 0.06 | 0.04 | 0.03 | 0.02 | 0.04 | 0.06 | 0.10 | 0.03 | 0.03 | 0.04 | 0.08 | 0.02 | 0.01 | 0.00 | 0.02 | 0.03 | 0.25 | 0.04 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.05 | 0.04 | 0.12 | 0.11 | 0.00 | 0.01 | 0.04 | 0.03 | 0.06 | 0.05 | 0.02 | 0.13 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.01 |
| STYXL1 | ENSG00000127952 | 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 | 0.10 | 0.01 | 0.05 | 0.03 | 0.14 | 0.02 | 0.12 | 0.01 | 0.01 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.05 | 0.01 | 0.00 | 0.01 | 0.12 | 0.00 | 0.00 | 0.02 | 0.00 | 0.01 | 0.07 | 0.02 | 0.19 | 0.07 | 0.05 | 0.01 | 0.04 | 0.02 | 0.06 | 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 |
| OAS1 | ENSG00000089127 | 0.01 | 0.01 | 0.02 | 0.00 | 0.06 | 0.02 | 0.03 | 0.03 | 0.12 | 0.02 | 0.00 | 0.00 | 0.02 | 0.01 | 0.02 | 0.05 | 0.04 | 0.04 | 0.01 | 0.03 | 0.08 | 0.05 | 0.06 | 0.02 | 0.00 | 0.02 | 0.05 | 0.01 | 0.00 | 0.06 | 0.03 | 0.05 | 0.00 | 0.22 | 0.12 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.02 | 0.08 | 0.10 | 0.21 | 0.02 | 0.02 | 0.03 | 0.05 | 0.10 | 0.08 | 0.15 | 0.05 | 0.02 | 0.00 | 0.00 | 0.00 | 0.10 | 0.00 | 0.01 | 0.03 | 0.01 | 0.01 | 0.00 | 0.00 | 0.03 | 0.06 |
| TPCN1 | ENSG00000186815 | 0.01 | 0.01 | 0.02 | 0.00 | 0.06 | 0.02 | 0.03 | 0.03 | 0.13 | 0.02 | 0.00 | 0.00 | 0.02 | 0.00 | 0.03 | 0.05 | 0.03 | 0.04 | 0.01 | 0.02 | 0.08 | 0.05 | 0.06 | 0.02 | 0.01 | 0.02 | 0.05 | 0.01 | 0.00 | 0.06 | 0.02 | 0.05 | 0.00 | 0.22 | 0.17 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.02 | 0.09 | 0.12 | 0.21 | 0.02 | 0.02 | 0.03 | 0.05 | 0.08 | 0.08 | 0.21 | 0.06 | 0.02 | 0.00 | 0.00 | 0.00 | 0.10 | 0.00 | 0.01 | 0.03 | 0.01 | 0.01 | 0.00 | 0.00 | 0.02 | 0.06 |
| XPNPEP3 | ENSG00000196236 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.00 | 0.01 | 0.01 | 0.09 | 0.00 | 0.03 | 0.00 | 0.04 | 0.04 | 0.03 | 0.06 | 0.02 | 0.03 | 0.02 | 0.04 | 0.00 | 0.02 | 0.01 | 0.01 | 0.01 | 0.01 | 0.05 | 0.04 | 0.03 | 0.04 | 0.01 | 0.04 | 0.01 | 0.02 | 0.00 | 0.00 | 0.06 | 0.00 | 0.00 | 0.03 | 0.03 | 0.03 | 0.22 | 0.04 | 0.04 | 0.06 | 0.05 | 0.16 | 0.15 | 0.07 | 0.04 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.05 | 0.00 | 0.00 | 0.30 | 0.00 |
| SLC2A14 | ENSG00000173262 | 0.01 | 0.01 | 0.00 | 0.01 | 0.02 | 0.00 | 0.01 | 0.07 | 0.09 | 0.03 | 0.01 | 0.00 | 0.00 | 0.05 | 0.06 | 0.07 | 0.14 | 0.01 | 0.11 | 0.02 | 0.10 | 0.02 | 0.04 | 0.07 | 0.04 | 0.03 | 0.08 | 0.03 | 0.05 | 0.07 | 0.02 | 0.05 | 0.14 | 0.05 | 0.05 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.11 | 0.04 | 0.32 | 0.08 | 0.03 | 0.02 | 0.03 | 0.03 | 0.00 | 0.03 | 0.14 | 0.11 | 0.57 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.12 | 0.01 | 0.03 | 0.02 | 0.00 | 0.01 | 0.04 | 0.04 |
| NOX5 | ENSG00000255346 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.01 | 0.02 | 0.02 | 0.02 | 0.00 | 0.00 | 0.09 | 0.00 | 0.04 | 0.02 | 0.05 | 0.02 | 0.02 | 0.02 | 0.05 | 0.02 | 0.05 | 0.02 | 0.01 | 0.01 | 0.01 | 0.03 | 0.03 | 0.01 | 0.02 | 0.02 | 0.00 | 0.01 | 0.04 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.04 | 0.15 | 0.10 | 0.08 | 0.02 | 0.02 | 0.03 | 0.12 | 0.12 | 0.12 | 0.04 | 0.01 | 0.01 | 0.00 | 0.00 | 0.06 | 0.00 | 0.01 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.10 | 0.00 |
| CCNT1 | ENSG00000129315 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.03 | 0.03 | 0.00 | 0.00 | 0.00 | 0.04 | 0.06 | 0.02 | 0.04 | 0.02 | 0.01 | 0.04 | 0.06 | 0.04 | 0.05 | 0.04 | 0.02 | 0.00 | 0.02 | 0.02 | 0.00 | 0.04 | 0.01 | 0.01 | 0.09 | 0.01 | 0.16 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.03 | 0.05 | 0.08 | 0.06 | 0.02 | 0.00 | 0.03 | 0.01 | 0.13 | 0.13 | 0.07 | 0.08 | 0.02 | 0.00 | 0.00 | 0.01 | 0.10 | 0.06 | 0.01 | 0.04 | 0.03 | 0.05 | 0.00 | 0.00 | 0.09 | 0.04 |
| NPFFR2 | ENSG00000056291 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.00 | 0.17 | 0.01 | 0.00 | 0.00 | 0.00 | 0.07 | 0.07 | 0.03 | 0.22 | 0.01 | 0.09 | 0.01 | 0.13 | 0.02 | 0.06 | 0.01 | 0.01 | 0.01 | 0.03 | 0.01 | 0.00 | 0.01 | 0.02 | 0.07 | 0.00 | 0.03 | 0.06 | 0.00 | 0.02 | 0.02 | 0.00 | 0.00 | 0.12 | 0.02 | 0.33 | 0.09 | 0.04 | 0.03 | 0.04 | 0.02 | 0.09 | 0.05 | 0.08 | 0.05 | 0.11 | 0.00 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.02 | 0.00 | 0.02 | 0.00 | 0.00 | 0.02 | 0.03 |
| TAB1 | ENSG00000100324 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.07 | 0.06 | 0.00 | 0.04 | 0.00 | 0.02 | 0.05 | 0.03 | 0.09 | 0.02 | 0.03 | 0.01 | 0.01 | 0.00 | 0.02 | 0.02 | 0.01 | 0.02 | 0.01 | 0.02 | 0.02 | 0.02 | 0.03 | 0.02 | 0.00 | 0.01 | 0.02 | 0.01 | 0.01 | 0.05 | 0.00 | 0.00 | 0.03 | 0.02 | 0.08 | 0.15 | 0.03 | 0.02 | 0.08 | 0.02 | 0.17 | 0.15 | 0.06 | 0.03 | 0.02 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.02 | 0.01 | 0.04 | 0.02 | 0.00 | 0.21 | 0.00 |
| TPH1 | ENSG00000129167 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.03 | 0.01 | 0.01 | 0.02 | 0.07 | 0.00 | 0.00 | 0.02 | 0.03 | 0.03 | 0.04 | 0.06 | 0.07 | 0.01 | 0.04 | 0.05 | 0.03 | 0.02 | 0.02 | 0.02 | 0.00 | 0.01 | 0.01 | 0.00 | 0.02 | 0.04 | 0.01 | 0.03 | 0.01 | 0.00 | 0.02 | 0.06 | 0.03 | 0.00 | 0.00 | 0.06 | 0.05 | 0.04 | 0.24 | 0.01 | 0.04 | 0.03 | 0.04 | 0.01 | 0.04 | 0.05 | 0.07 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.03 | 0.01 |
| SVOPL | ENSG00000157703 | 0.01 | 0.01 | 0.09 | 0.00 | 0.06 | 0.00 | 0.03 | 0.02 | 0.04 | 0.03 | 0.00 | 0.01 | 0.04 | 0.05 | 0.08 | 0.02 | 0.08 | 0.07 | 0.03 | 0.14 | 0.04 | 0.19 | 0.03 | 0.07 | 0.03 | 0.00 | 0.03 | 0.01 | 0.01 | 0.05 | 0.05 | 0.04 | 0.00 | 0.02 | 0.03 | 0.06 | 0.00 | 0.01 | 0.00 | 0.00 | 0.08 | 0.04 | 0.50 | 0.04 | 0.04 | 0.08 | 0.05 | 0.05 | 0.08 | 0.14 | 0.11 | 0.08 | 0.02 | 0.04 | 0.00 | 0.05 | 0.02 | 0.09 | 0.11 | 0.01 | 0.05 | 0.01 | 0.00 | 0.00 | 0.22 | 0.02 |
| CD226 | ENSG00000150637 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.11 | 0.01 | 0.10 | 0.00 | 0.00 | 0.00 | 0.06 | 0.05 | 0.09 | 0.03 | 0.08 | 0.01 | 0.15 | 0.02 | 0.17 | 0.03 | 0.16 | 0.00 | 0.13 | 0.02 | 0.08 | 0.01 | 0.07 | 0.03 | 0.06 | 0.00 | 0.10 | 0.04 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.07 | 0.08 | 0.38 | 0.01 | 0.04 | 0.02 | 0.08 | 0.04 | 0.19 | 0.11 | 0.09 | 0.00 | 0.12 | 0.00 | 0.01 | 0.10 | 0.00 | 0.01 | 0.02 | 0.00 | 0.06 | 0.00 | 0.04 | 0.03 | 0.02 |
| TLK1 | ENSG00000198586 | 0.02 | 0.00 | 0.05 | 0.00 | 0.00 | 0.00 | 0.01 | 0.09 | 0.05 | 0.05 | 0.00 | 0.01 | 0.00 | 0.00 | 0.06 | 0.01 | 0.13 | 0.02 | 0.10 | 0.01 | 0.19 | 0.02 | 0.05 | 0.04 | 0.01 | 0.01 | 0.03 | 0.03 | 0.03 | 0.01 | 0.05 | 0.06 | 0.00 | 0.01 | 0.04 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.03 | 0.36 | 0.04 | 0.10 | 0.01 | 0.06 | 0.01 | 0.03 | 0.00 | 0.04 | 0.10 | 0.04 | 0.01 | 0.00 | 0.00 | 0.00 | 0.07 | 0.01 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.02 | 0.02 |
| NEK7 | ENSG00000151414 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.12 | 0.05 | 0.02 | 0.00 | 0.10 | 0.00 | 0.11 | 0.01 | 0.09 | 0.02 | 0.05 | 0.01 | 0.13 | 0.06 | 0.05 | 0.01 | 0.03 | 0.00 | 0.11 | 0.03 | 0.01 | 0.00 | 0.23 | 0.01 | 0.20 | 0.02 | 0.06 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.21 | 0.01 | 0.28 | 0.06 | 0.07 | 0.00 | 0.08 | 0.01 | 0.07 | 0.03 | 0.10 | 0.10 | 0.06 | 0.00 | 0.01 | 0.01 | 0.26 | 0.02 | 0.00 | 0.01 | 0.01 | 0.01 | 0.06 | 0.00 | 0.17 | 0.02 |
| GALNT1 | ENSG00000141429 | 0.00 | 0.00 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.02 | 0.06 | 0.03 | 0.00 | 0.00 | 0.03 | 0.00 | 0.15 | 0.03 | 0.12 | 0.01 | 0.06 | 0.04 | 0.16 | 0.06 | 0.08 | 0.06 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.04 | 0.02 | 0.01 | 0.00 | 0.01 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.23 | 0.09 | 0.01 | 0.01 | 0.03 | 0.01 | 0.12 | 0.03 | 0.10 | 0.05 | 0.01 | 0.03 | 0.00 | 0.01 | 0.03 | 0.00 | 0.02 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.03 | 0.01 |
| COL9A1 | ENSG00000112280 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.14 | 0.06 | 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 | 0.05 | 0.05 | 0.02 | 0.02 | 0.01 | 0.00 | 0.01 | 0.02 | 0.05 | 0.04 | 0.00 | 0.14 | 0.04 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.07 | 0.07 | 0.14 | 0.10 | 0.01 | 0.02 | 0.03 | 0.01 | 0.06 | 0.08 | 0.05 | 0.15 | 0.04 | 0.00 | 0.00 | 0.00 | 0.02 | 0.06 | 0.00 | 0.01 | 0.01 | 0.04 | 0.05 | 0.00 | 0.04 | 0.04 |
| NOS1 | ENSG00000089250 | 0.01 | 0.01 | 0.02 | 0.00 | 0.06 | 0.02 | 0.04 | 0.03 | 0.13 | 0.02 | 0.00 | 0.00 | 0.03 | 0.00 | 0.03 | 0.05 | 0.03 | 0.05 | 0.03 | 0.02 | 0.09 | 0.04 | 0.06 | 0.02 | 0.01 | 0.01 | 0.04 | 0.02 | 0.01 | 0.06 | 0.04 | 0.05 | 0.00 | 0.22 | 0.05 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.03 | 0.08 | 0.14 | 0.20 | 0.04 | 0.02 | 0.02 | 0.05 | 0.09 | 0.08 | 0.18 | 0.06 | 0.01 | 0.02 | 0.00 | 0.01 | 0.10 | 0.00 | 0.03 | 0.01 | 0.01 | 0.00 | 0.09 | 0.00 | 0.03 | 0.07 |
| CHD6 | ENSG00000124177 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.01 | 0.09 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.03 | 0.04 | 0.08 | 0.01 | 0.01 | 0.02 | 0.08 | 0.01 | 0.09 | 0.00 | 0.10 | 0.01 | 0.13 | 0.00 | 0.01 | 0.00 | 0.02 | 0.01 | 0.00 | 0.04 | 0.08 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.08 | 0.03 | 0.06 | 0.09 | 0.02 | 0.02 | 0.05 | 0.01 | 0.17 | 0.04 | 0.18 | 0.03 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.05 | 0.01 |
| SSTR3 | ENSG00000278195 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.11 | 0.05 | 0.00 | 0.04 | 0.00 | 0.07 | 0.06 | 0.04 | 0.07 | 0.02 | 0.01 | 0.01 | 0.03 | 0.02 | 0.02 | 0.02 | 0.01 | 0.01 | 0.02 | 0.01 | 0.03 | 0.01 | 0.06 | 0.01 | 0.00 | 0.01 | 0.02 | 0.02 | 0.00 | 0.04 | 0.00 | 0.00 | 0.03 | 0.02 | 0.10 | 0.11 | 0.03 | 0.01 | 0.05 | 0.02 | 0.30 | 0.06 | 0.04 | 0.02 | 0.02 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.00 | 0.03 | 0.00 | 0.00 | 0.13 | 0.01 |
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