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 |
| CRLF2 | ENSG00000205755 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |
| CRYZL1 | ENSG00000205758 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.07 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.03 | 0.02 | 0.03 | 0.02 | 0.06 | 0.02 | 0.03 | 0.01 | 0.06 | 0.01 | 0.03 | 0.01 | 0.01 | 0.05 | 0.01 | 0.01 | 0.01 | 0.01 | 0.05 | 0.03 | 0.12 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.05 | 0.02 | 0.11 | 0.05 | 0.02 | 0.03 | 0.03 | 0.01 | 0.07 | 0.03 | 0.04 | 0.06 | 0.02 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.01 | 0.03 | 0.00 | 0.01 | 0.01 |
| KLRC2 | ENSG00000205809 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.03 | 0.01 | 0.13 | 0.06 | 0.05 | 0.01 | 0.00 | 0.00 | 0.05 | 0.03 | 0.09 | 0.12 | 0.01 | 0.10 | 0.02 | 0.05 | 0.02 | 0.05 | 0.08 | 0.01 | 0.03 | 0.04 | 0.04 | 0.01 | 0.06 | 0.01 | 0.05 | 0.14 | 0.05 | 0.03 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.10 | 0.05 | 0.31 | 0.10 | 0.01 | 0.02 | 0.03 | 0.03 | 0.03 | 0.03 | 0.11 | 0.12 | 0.56 | 0.00 | 0.00 | 0.03 | 0.00 | 0.08 | 0.10 | 0.01 | 0.02 | 0.05 | 0.00 | 0.01 | 0.05 | 0.03 |
| C1QTNF9B | ENSG00000205863 | 0.02 | 0.02 | 0.01 | 0.01 | 0.00 | 0.00 | 0.03 | 0.05 | 0.08 | 0.06 | 0.00 | 0.02 | 0.00 | 0.17 | 0.01 | 0.11 | 0.02 | 0.12 | 0.01 | 0.16 | 0.09 | 0.10 | 0.08 | 0.04 | 0.21 | 0.00 | 0.22 | 0.03 | 0.00 | 0.01 | 0.04 | 0.12 | 0.00 | 0.15 | 0.00 | 0.09 | 0.00 | 0.01 | 0.00 | 0.01 | 0.08 | 0.08 | 0.11 | 0.20 | 0.03 | 0.15 | 0.02 | 0.05 | 0.01 | 0.16 | 0.12 | 0.20 | 0.00 | 0.01 | 0.00 | 0.00 | 0.04 | 0.11 | 0.00 | 0.06 | 0.01 | 0.07 | 0.00 | 0.00 | 0.05 | 0.04 |
| DEFA1 | ENSG00000206047 | 0.00 | 0.02 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.12 | 0.01 | 0.15 | 0.00 | 0.00 | 0.02 | 0.04 | 0.03 | 0.07 | 0.01 | 0.14 | 0.00 | 0.08 | 0.16 | 0.08 | 0.17 | 0.04 | 0.01 | 0.10 | 0.00 | 0.20 | 0.03 | 0.05 | 0.01 | 0.14 | 0.00 | 0.01 | 0.00 | 0.02 | 0.00 | 0.02 | 0.00 | 0.00 | 0.02 | 0.16 | 0.04 | 0.42 | 0.01 | 0.05 | 0.00 | 0.09 | 0.03 | 0.28 | 0.05 | 0.13 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.08 | 0.00 | 0.01 | 0.01 | 0.02 | 0.00 | 0.01 | 0.02 | 0.03 |
| SERPINB11 | ENSG00000206072 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.10 | 0.02 | 0.09 | 0.00 | 0.00 | 0.00 | 0.02 | 0.03 | 0.09 | 0.05 | 0.06 | 0.03 | 0.14 | 0.05 | 0.20 | 0.02 | 0.16 | 0.00 | 0.12 | 0.01 | 0.11 | 0.01 | 0.08 | 0.02 | 0.06 | 0.00 | 0.10 | 0.03 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.08 | 0.05 | 0.09 | 0.33 | 0.05 | 0.03 | 0.00 | 0.07 | 0.01 | 0.11 | 0.13 | 0.07 | 0.00 | 0.07 | 0.00 | 0.00 | 0.10 | 0.00 | 0.01 | 0.02 | 0.00 | 0.04 | 0.00 | 0.01 | 0.03 | 0.01 |
| SERPINB4 | ENSG00000206073 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.10 | 0.02 | 0.09 | 0.00 | 0.00 | 0.00 | 0.02 | 0.03 | 0.09 | 0.05 | 0.06 | 0.02 | 0.14 | 0.05 | 0.20 | 0.02 | 0.16 | 0.00 | 0.12 | 0.01 | 0.11 | 0.00 | 0.08 | 0.02 | 0.06 | 0.00 | 0.10 | 0.01 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.08 | 0.05 | 0.09 | 0.33 | 0.04 | 0.03 | 0.00 | 0.07 | 0.01 | 0.09 | 0.13 | 0.07 | 0.00 | 0.07 | 0.00 | 0.00 | 0.10 | 0.00 | 0.01 | 0.02 | 0.00 | 0.04 | 0.00 | 0.01 | 0.03 | 0.01 |
| RNASE13 | ENSG00000206150 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.02 | 0.09 | 0.06 | 0.00 | 0.00 | 0.00 | 0.05 | 0.14 | 0.03 | 0.14 | 0.08 | 0.10 | 0.06 | 0.09 | 0.07 | 0.09 | 0.04 | 0.03 | 0.02 | 0.01 | 0.08 | 0.01 | 0.05 | 0.09 | 0.00 | 0.00 | 0.02 | 0.28 | 0.03 | 0.01 | 0.02 | 0.00 | 0.00 | 0.09 | 0.03 | 0.44 | 0.10 | 0.07 | 0.01 | 0.09 | 0.03 | 0.16 | 0.08 | 0.18 | 0.09 | 0.02 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.03 | 0.03 | 0.10 | 0.00 | 0.00 | 0.03 | 0.02 |
| ATP10A | ENSG00000206190 | 0.01 | 0.01 | 0.00 | 0.02 | 0.14 | 0.00 | 0.06 | 0.03 | 0.08 | 0.10 | 0.00 | 0.00 | 0.00 | 0.21 | 0.02 | 0.12 | 0.06 | 0.10 | 0.05 | 0.04 | 0.12 | 0.10 | 0.01 | 0.09 | 0.01 | 0.08 | 0.02 | 0.05 | 0.00 | 0.03 | 0.01 | 0.04 | 0.00 | 0.04 | 0.09 | 0.08 | 0.00 | 0.00 | 0.00 | 0.00 | 0.07 | 0.12 | 0.10 | 0.27 | 0.07 | 0.04 | 0.02 | 0.06 | 0.11 | 0.46 | 0.09 | 0.10 | 0.04 | 0.03 | 0.04 | 0.00 | 0.00 | 0.04 | 0.02 | 0.02 | 0.01 | 0.06 | 0.00 | 0.00 | 0.03 | 0.10 |
| TSSK2 | ENSG00000206203 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.05 | 0.17 | 0.06 | 0.03 | 0.01 | 0.08 | 0.05 | 0.07 | 0.03 | 0.17 | 0.07 | 0.10 | 0.03 | 0.08 | 0.07 | 0.05 | 0.04 | 0.02 | 0.01 | 0.06 | 0.03 | 0.00 | 0.02 | 0.02 | 0.03 | 0.08 | 0.10 | 0.10 | 0.14 | 0.01 | 0.01 | 0.02 | 0.00 | 0.06 | 0.05 | 0.19 | 0.07 | 0.05 | 0.01 | 0.06 | 0.06 | 0.42 | 0.04 | 0.14 | 0.07 | 0.13 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.01 | 0.03 | 0.00 | 0.00 | 0.13 | 0.03 |
| OR10C1 | ENSG00000206474 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.15 | 0.02 | 0.00 | 0.00 | 0.02 | 0.02 | 0.08 | 0.02 | 0.06 | 0.05 | 0.03 | 0.04 | 0.15 | 0.08 | 0.09 | 0.04 | 0.04 | 0.02 | 0.06 | 0.01 | 0.04 | 0.02 | 0.10 | 0.01 | 0.06 | 0.03 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.09 | 0.02 | 0.31 | 0.05 | 0.09 | 0.03 | 0.03 | 0.01 | 0.26 | 0.02 | 0.03 | 0.05 | 0.01 | 0.01 | 0.00 | 0.00 | 0.05 | 0.10 | 0.01 | 0.01 | 0.00 | 0.01 | 0.13 | 0.00 | 0.13 | 0.01 |
| OR5K3 | ENSG00000206536 | 0.01 | 0.01 | 0.02 | 0.01 | 0.00 | 0.00 | 0.02 | 0.02 | 0.05 | 0.02 | 0.00 | 0.00 | 0.01 | 0.04 | 0.06 | 0.02 | 0.17 | 0.03 | 0.06 | 0.01 | 0.11 | 0.03 | 0.05 | 0.04 | 0.00 | 0.01 | 0.03 | 0.01 | 0.00 | 0.01 | 0.02 | 0.02 | 0.00 | 0.12 | 0.10 | 0.02 | 0.00 | 0.06 | 0.00 | 0.00 | 0.05 | 0.02 | 0.23 | 0.04 | 0.05 | 0.02 | 0.04 | 0.00 | 0.18 | 0.08 | 0.07 | 0.06 | 0.04 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.04 | 0.00 | 0.03 | 0.00 | 0.00 | 0.01 | 0.01 |
| PRSS50 | ENSG00000206549 | 0.00 | 0.18 | 0.00 | 0.02 | 0.08 | 0.00 | 0.00 | 0.03 | 0.05 | 0.10 | 0.00 | 0.04 | 0.00 | 0.54 | 0.01 | 0.06 | 0.01 | 0.09 | 0.00 | 0.05 | 0.01 | 0.08 | 0.02 | 0.11 | 0.00 | 0.05 | 0.03 | 0.06 | 0.00 | 0.05 | 0.04 | 0.04 | 0.00 | 0.24 | 0.03 | 0.02 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.15 | 0.08 | 0.19 | 0.01 | 0.05 | 0.03 | 0.05 | 0.03 | 0.25 | 0.05 | 0.11 | 0.01 | 0.04 | 0.00 | 0.01 | 0.00 | 0.10 | 0.00 | 0.05 | 0.00 | 0.04 | 0.00 | 0.03 | 0.01 | 0.05 |
| GPX3 | ENSG00000211445 | 0.30 | 0.00 | 0.02 | 0.01 | 0.03 | 0.00 | 0.02 | 0.01 | 0.02 | 0.05 | 0.00 | 0.00 | 0.02 | 0.05 | 0.04 | 0.05 | 0.01 | 0.03 | 0.01 | 0.04 | 0.03 | 0.01 | 0.03 | 0.03 | 0.01 | 0.02 | 0.04 | 0.01 | 0.02 | 0.02 | 0.10 | 0.02 | 0.09 | 0.01 | 0.26 | 0.04 | 0.00 | 0.03 | 0.01 | 0.00 | 0.04 | 0.03 | 0.17 | 0.12 | 0.02 | 0.01 | 0.03 | 0.02 | 0.05 | 0.02 | 0.07 | 0.07 | 0.00 | 0.00 | 0.00 | 0.09 | 0.04 | 0.03 | 0.01 | 0.06 | 0.01 | 0.03 | 0.00 | 0.03 | 0.03 | 0.14 |
| DIO2 | ENSG00000211448 | 0.00 | 0.03 | 0.01 | 0.01 | 0.00 | 0.01 | 0.01 | 0.04 | 0.04 | 0.05 | 0.00 | 0.00 | 0.01 | 0.06 | 0.03 | 0.05 | 0.06 | 0.03 | 0.04 | 0.02 | 0.07 | 0.05 | 0.03 | 0.04 | 0.00 | 0.04 | 0.01 | 0.03 | 0.01 | 0.01 | 0.01 | 0.09 | 0.00 | 0.31 | 0.01 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.02 | 0.09 | 0.15 | 0.18 | 0.05 | 0.05 | 0.03 | 0.02 | 0.05 | 0.06 | 0.07 | 0.12 | 0.03 | 0.01 | 0.00 | 0.00 | 0.04 | 0.00 | 0.00 | 0.11 | 0.01 | 0.07 | 0.03 | 0.00 | 0.01 | 0.06 |
| GNRHR2 | ENSG00000211451 | 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 |
| DIO1 | ENSG00000211452 | 0.00 | 0.01 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.06 | 0.09 | 0.04 | 0.00 | 0.00 | 0.06 | 0.04 | 0.06 | 0.04 | 0.05 | 0.03 | 0.04 | 0.04 | 0.08 | 0.03 | 0.02 | 0.04 | 0.01 | 0.04 | 0.00 | 0.04 | 0.01 | 0.01 | 0.03 | 0.05 | 0.00 | 0.25 | 0.02 | 0.03 | 0.00 | 0.17 | 0.00 | 0.00 | 0.08 | 0.04 | 0.34 | 0.10 | 0.08 | 0.02 | 0.05 | 0.02 | 0.06 | 0.04 | 0.19 | 0.03 | 0.05 | 0.03 | 0.02 | 0.00 | 0.00 | 0.07 | 0.00 | 0.01 | 0.02 | 0.02 | 0.00 | 0.07 | 0.05 | 0.03 |
| AKR7L | ENSG00000211454 | 0.00 | 0.06 | 0.00 | 0.08 | 0.00 | 0.00 | 0.01 | 0.04 | 0.07 | 0.08 | 0.00 | 0.01 | 0.04 | 0.25 | 0.04 | 0.06 | 0.04 | 0.11 | 0.03 | 0.08 | 0.05 | 0.09 | 0.06 | 0.11 | 0.00 | 0.16 | 0.00 | 0.22 | 0.02 | 0.07 | 0.02 | 0.23 | 0.00 | 1.11 | 0.01 | 0.08 | 0.01 | 0.10 | 0.00 | 0.00 | 0.02 | 0.21 | 0.10 | 0.44 | 0.04 | 0.08 | 0.05 | 0.13 | 0.03 | 0.15 | 0.18 | 0.12 | 0.05 | 0.07 | 0.02 | 0.01 | 0.00 | 0.03 | 0.00 | 0.02 | 0.03 | 0.08 | 0.00 | 0.12 | 0.06 | 0.09 |
| SLC48A1 | ENSG00000211584 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.09 | 0.03 | 0.00 | 0.00 | 0.00 | 0.04 | 0.05 | 0.02 | 0.08 | 0.02 | 0.02 | 0.03 | 0.07 | 0.04 | 0.05 | 0.03 | 0.02 | 0.00 | 0.02 | 0.02 | 0.00 | 0.04 | 0.02 | 0.01 | 0.00 | 0.01 | 0.21 | 0.01 | 0.02 | 0.03 | 0.00 | 0.00 | 0.04 | 0.05 | 0.18 | 0.06 | 0.05 | 0.00 | 0.15 | 0.01 | 0.38 | 0.10 | 0.26 | 0.08 | 0.02 | 0.02 | 0.00 | 0.03 | 0.13 | 0.04 | 0.01 | 0.05 | 0.02 | 0.06 | 0.00 | 0.00 | 0.05 | 0.05 |
| IGKV4-1 | ENSG00000211598 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.03 | 0.07 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.03 | 0.02 | 0.09 | 0.02 | 0.07 | 0.02 | 0.10 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.02 | 0.00 | 0.01 | 0.02 | 0.02 | 0.00 | 0.02 | 0.08 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.04 | 0.02 | 0.11 | 0.05 | 0.04 | 0.01 | 0.05 | 0.02 | 0.08 | 0.02 | 0.20 | 0.05 | 0.01 | 0.04 | 0.00 | 0.00 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.03 | 0.01 |
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