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 |
| MOCS3 | ENSG00000124217 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.00 | 0.14 | 0.01 | 0.00 | 0.00 | 0.03 | 0.00 | 0.10 | 0.03 | 0.14 | 0.01 | 0.01 | 0.01 | 0.09 | 0.01 | 0.19 | 0.00 | 0.11 | 0.00 | 0.08 | 0.00 | 0.02 | 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 | 0.33 | 0.03 | 0.02 | 0.03 | 0.08 | 0.01 | 0.24 | 0.00 | 0.14 | 0.03 | 0.02 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.12 | 0.00 |
| SEMG1 | ENSG00000124233 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.01 | 0.21 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.05 | 0.09 | 0.01 | 0.01 | 0.02 | 0.12 | 0.00 | 0.21 | 0.00 | 0.19 | 0.00 | 0.14 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.00 | 0.04 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.14 | 0.02 | 0.25 | 0.05 | 0.03 | 0.05 | 0.10 | 0.01 | 0.45 | 0.00 | 0.11 | 0.03 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.06 | 0.01 |
| KCNK15 | ENSG00000124249 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.23 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.05 | 0.07 | 0.01 | 0.02 | 0.02 | 0.14 | 0.00 | 0.20 | 0.00 | 0.19 | 0.00 | 0.14 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.00 | 0.04 | 0.04 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.11 | 0.02 | 0.20 | 0.05 | 0.02 | 0.04 | 0.08 | 0.01 | 0.42 | 0.00 | 0.11 | 0.03 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.05 | 0.01 |
| VAMP7 | ENSG00000124333 | 0.03 | 0.02 | 0.02 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.10 | 0.04 | 0.06 | 0.00 | 0.06 | 0.03 | 0.24 | 0.01 | 0.18 | 0.04 | 0.14 | 0.01 | 0.19 | 0.02 | 0.17 | 0.04 | 0.05 | 0.01 | 0.09 | 0.01 | 0.06 | 0.00 | 0.11 | 0.03 | 0.10 | 0.02 | 0.13 | 0.02 | 0.00 | 0.01 | 0.00 | 0.01 | 0.10 | 0.03 | 0.43 | 0.13 | 0.24 | 0.02 | 0.08 | 0.04 | 0.09 | 0.10 | 0.21 | 0.13 | 0.01 | 0.03 | 0.00 | 0.00 | 0.11 | 0.07 | 0.03 | 0.03 | 0.03 | 0.02 | 0.05 | 0.00 | 0.07 | 0.01 |
| IL9R | ENSG00000124334 | 0.03 | 0.02 | 0.02 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.10 | 0.04 | 0.06 | 0.00 | 0.06 | 0.03 | 0.24 | 0.01 | 0.18 | 0.04 | 0.14 | 0.01 | 0.19 | 0.02 | 0.17 | 0.04 | 0.05 | 0.01 | 0.09 | 0.01 | 0.06 | 0.00 | 0.11 | 0.03 | 0.10 | 0.02 | 0.13 | 0.02 | 0.00 | 0.01 | 0.00 | 0.01 | 0.10 | 0.03 | 0.43 | 0.13 | 0.24 | 0.02 | 0.08 | 0.04 | 0.09 | 0.10 | 0.21 | 0.13 | 0.01 | 0.03 | 0.00 | 0.00 | 0.11 | 0.07 | 0.03 | 0.03 | 0.03 | 0.02 | 0.05 | 0.00 | 0.07 | 0.01 |
| IL17C | ENSG00000124391 | 0.00 | 0.00 | 0.00 | 0.04 | 0.00 | 0.06 | 0.01 | 0.25 | 0.08 | 0.05 | 0.00 | 0.00 | 0.00 | 0.19 | 0.02 | 0.12 | 0.03 | 0.06 | 0.04 | 0.04 | 0.09 | 0.05 | 0.05 | 0.05 | 0.02 | 0.03 | 0.02 | 0.03 | 0.02 | 0.01 | 0.02 | 0.08 | 0.05 | 0.05 | 0.07 | 0.06 | 0.00 | 0.02 | 0.00 | 0.01 | 0.05 | 0.09 | 0.05 | 0.34 | 0.05 | 0.08 | 0.02 | 0.08 | 0.03 | 0.29 | 0.06 | 0.10 | 0.00 | 0.12 | 0.00 | 0.04 | 0.03 | 0.00 | 0.00 | 0.02 | 0.01 | 0.05 | 0.00 | 0.02 | 0.02 | 0.10 |
| CEACAM8 | ENSG00000124469 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.02 | 0.00 | 0.08 | 0.14 | 0.03 | 0.00 | 0.00 | 0.15 | 0.07 | 0.11 | 0.05 | 0.13 | 0.08 | 0.02 | 0.02 | 0.02 | 0.07 | 0.05 | 0.02 | 0.02 | 0.02 | 0.02 | 0.03 | 0.02 | 0.03 | 0.05 | 0.03 | 0.12 | 0.01 | 0.14 | 0.04 | 0.00 | 0.02 | 0.00 | 0.00 | 0.06 | 0.05 | 0.18 | 0.28 | 0.11 | 0.05 | 0.05 | 0.05 | 0.13 | 0.17 | 0.20 | 0.12 | 0.00 | 0.04 | 0.01 | 0.00 | 0.05 | 0.06 | 0.01 | 0.12 | 0.03 | 0.09 | 0.00 | 0.00 | 0.02 | 0.03 |
| NDP | ENSG00000124479 | 0.01 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 | 0.03 | 0.03 | 0.01 | 0.00 | 0.00 | 0.02 | 0.08 | 0.01 | 0.04 | 0.04 | 0.01 | 0.04 | 0.09 | 0.06 | 0.03 | 0.01 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.02 | 0.00 | 0.01 | 0.00 | 0.01 | 0.13 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.04 | 0.01 | 0.16 | 0.07 | 0.01 | 0.03 | 0.04 | 0.01 | 0.29 | 0.05 | 0.10 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.08 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.02 | 0.00 |
| CRISP2 | ENSG00000124490 | 0.01 | 0.00 | 0.02 | 0.02 | 0.00 | 0.00 | 0.01 | 0.01 | 0.08 | 0.04 | 0.00 | 0.00 | 0.00 | 0.02 | 0.07 | 0.01 | 0.20 | 0.04 | 0.05 | 0.03 | 0.32 | 0.02 | 0.14 | 0.02 | 0.03 | 0.01 | 0.12 | 0.01 | 0.01 | 0.01 | 0.08 | 0.00 | 0.00 | 0.03 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.10 | 0.03 | 0.22 | 0.06 | 0.08 | 0.04 | 0.05 | 0.01 | 0.20 | 0.03 | 0.08 | 0.03 | 0.02 | 0.01 | 0.00 | 0.00 | 0.09 | 0.02 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 | 0.00 | 0.03 | 0.02 |
| BTN2A2 | ENSG00000124508 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.02 | 0.21 | 0.03 | 0.00 | 0.01 | 0.02 | 0.05 | 0.08 | 0.01 | 0.07 | 0.06 | 0.02 | 0.04 | 0.11 | 0.10 | 0.06 | 0.05 | 0.03 | 0.02 | 0.04 | 0.03 | 0.02 | 0.04 | 0.10 | 0.01 | 0.06 | 0.08 | 0.04 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.11 | 0.03 | 0.35 | 0.05 | 0.09 | 0.03 | 0.04 | 0.01 | 0.20 | 0.02 | 0.03 | 0.06 | 0.01 | 0.01 | 0.00 | 0.00 | 0.05 | 0.01 | 0.01 | 0.01 | 0.01 | 0.00 | 0.11 | 0.00 | 0.13 | 0.01 |
| BTN1A1 | ENSG00000124557 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.02 | 0.21 | 0.03 | 0.00 | 0.01 | 0.02 | 0.05 | 0.08 | 0.01 | 0.07 | 0.06 | 0.02 | 0.04 | 0.11 | 0.10 | 0.06 | 0.05 | 0.03 | 0.02 | 0.05 | 0.03 | 0.02 | 0.04 | 0.10 | 0.01 | 0.06 | 0.08 | 0.04 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.11 | 0.03 | 0.35 | 0.05 | 0.09 | 0.03 | 0.04 | 0.01 | 0.20 | 0.02 | 0.04 | 0.06 | 0.01 | 0.01 | 0.00 | 0.00 | 0.05 | 0.01 | 0.01 | 0.01 | 0.01 | 0.00 | 0.11 | 0.00 | 0.13 | 0.01 |
| SLC17A3 | ENSG00000124564 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.01 | 0.27 | 0.02 | 0.00 | 0.01 | 0.02 | 0.03 | 0.07 | 0.02 | 0.07 | 0.06 | 0.02 | 0.05 | 0.10 | 0.11 | 0.04 | 0.04 | 0.03 | 0.03 | 0.04 | 0.04 | 0.03 | 0.03 | 0.12 | 0.02 | 0.06 | 0.08 | 0.01 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.15 | 0.03 | 0.38 | 0.05 | 0.09 | 0.04 | 0.05 | 0.01 | 0.20 | 0.02 | 0.04 | 0.07 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.01 | 0.01 | 0.00 | 0.16 | 0.00 | 0.16 | 0.01 |
| OR2B6 | ENSG00000124657 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.02 | 0.19 | 0.02 | 0.00 | 0.00 | 0.02 | 0.05 | 0.06 | 0.02 | 0.07 | 0.06 | 0.02 | 0.04 | 0.09 | 0.09 | 0.07 | 0.05 | 0.04 | 0.02 | 0.06 | 0.02 | 0.02 | 0.03 | 0.10 | 0.01 | 0.06 | 0.01 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.09 | 0.03 | 0.33 | 0.06 | 0.08 | 0.04 | 0.04 | 0.01 | 0.26 | 0.02 | 0.04 | 0.06 | 0.01 | 0.01 | 0.00 | 0.00 | 0.05 | 0.01 | 0.01 | 0.01 | 0.00 | 0.01 | 0.13 | 0.00 | 0.14 | 0.01 |
| TREM1 | ENSG00000124731 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.15 | 0.03 | 0.01 | 0.00 | 0.02 | 0.03 | 0.14 | 0.01 | 0.10 | 0.05 | 0.05 | 0.02 | 0.43 | 0.02 | 0.27 | 0.01 | 0.09 | 0.00 | 0.12 | 0.00 | 0.04 | 0.00 | 0.07 | 0.00 | 0.05 | 0.03 | 0.07 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.11 | 0.03 | 0.30 | 0.05 | 0.05 | 0.02 | 0.05 | 0.01 | 0.06 | 0.03 | 0.22 | 0.03 | 0.05 | 0.01 | 0.00 | 0.00 | 0.14 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.04 | 0.00 | 0.04 | 0.00 |
| CDKN1A | ENSG00000124762 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.05 | 0.01 | 0.01 | 0.10 | 0.05 | 0.00 | 0.00 | 0.02 | 0.01 | 0.08 | 0.01 | 0.05 | 0.04 | 0.02 | 0.03 | 0.16 | 0.03 | 0.08 | 0.03 | 0.02 | 0.01 | 0.07 | 0.01 | 0.01 | 0.01 | 0.04 | 0.04 | 0.05 | 0.03 | 0.07 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.09 | 0.03 | 0.31 | 0.05 | 0.08 | 0.01 | 0.08 | 0.01 | 0.30 | 0.03 | 0.05 | 0.09 | 0.05 | 0.01 | 0.00 | 0.00 | 0.08 | 0.00 | 0.01 | 0.00 | 0.02 | 0.00 | 0.10 | 0.00 | 0.08 | 0.01 |
| GLO1 | ENSG00000124767 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.12 | 0.03 | 0.01 | 0.00 | 0.02 | 0.01 | 0.09 | 0.02 | 0.07 | 0.04 | 0.04 | 0.02 | 0.27 | 0.03 | 0.13 | 0.02 | 0.06 | 0.01 | 0.08 | 0.00 | 0.01 | 0.01 | 0.06 | 0.01 | 0.05 | 0.03 | 0.03 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.09 | 0.03 | 0.31 | 0.05 | 0.05 | 0.02 | 0.04 | 0.01 | 0.22 | 0.03 | 0.11 | 0.06 | 0.05 | 0.01 | 0.00 | 0.00 | 0.11 | 0.00 | 0.02 | 0.00 | 0.01 | 0.00 | 0.10 | 0.00 | 0.08 | 0.00 |
| KCNK17 | ENSG00000124780 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.11 | 0.03 | 0.00 | 0.00 | 0.02 | 0.02 | 0.11 | 0.01 | 0.09 | 0.05 | 0.03 | 0.02 | 0.25 | 0.03 | 0.13 | 0.02 | 0.05 | 0.01 | 0.07 | 0.00 | 0.03 | 0.01 | 0.06 | 0.00 | 0.05 | 0.03 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.09 | 0.03 | 0.30 | 0.05 | 0.05 | 0.01 | 0.04 | 0.01 | 0.09 | 0.03 | 0.11 | 0.05 | 0.05 | 0.01 | 0.00 | 0.00 | 0.14 | 0.00 | 0.02 | 0.00 | 0.02 | 0.01 | 0.09 | 0.00 | 0.05 | 0.00 |
| SSR1 | ENSG00000124783 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.07 | 0.29 | 0.05 | 0.00 | 0.06 | 0.02 | 0.01 | 0.10 | 0.01 | 0.10 | 0.08 | 0.06 | 0.06 | 0.08 | 0.22 | 0.06 | 0.11 | 0.02 | 0.03 | 0.02 | 0.04 | 0.00 | 0.08 | 0.15 | 0.02 | 0.06 | 0.06 | 0.02 | 0.06 | 0.00 | 0.01 | 0.00 | 0.00 | 0.14 | 0.06 | 0.47 | 0.09 | 0.10 | 0.06 | 0.10 | 0.02 | 0.19 | 0.05 | 0.10 | 0.14 | 0.04 | 0.03 | 0.00 | 0.00 | 0.10 | 0.01 | 0.02 | 0.03 | 0.01 | 0.03 | 0.28 | 0.00 | 0.25 | 0.00 |
| CRISP1 | ENSG00000124812 | 0.00 | 0.01 | 0.02 | 0.02 | 0.00 | 0.00 | 0.01 | 0.01 | 0.09 | 0.04 | 0.00 | 0.00 | 0.00 | 0.02 | 0.08 | 0.02 | 0.21 | 0.04 | 0.05 | 0.03 | 0.28 | 0.02 | 0.16 | 0.01 | 0.02 | 0.01 | 0.12 | 0.01 | 0.01 | 0.01 | 0.08 | 0.00 | 0.00 | 0.03 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.11 | 0.03 | 0.20 | 0.06 | 0.08 | 0.04 | 0.04 | 0.01 | 0.20 | 0.03 | 0.08 | 0.03 | 0.02 | 0.01 | 0.00 | 0.00 | 0.09 | 0.02 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 | 0.00 | 0.03 | 0.02 |
| OPN5 | ENSG00000124818 | 0.00 | 0.00 | 0.01 | 0.02 | 0.00 | 0.00 | 0.02 | 0.02 | 0.07 | 0.03 | 0.00 | 0.00 | 0.00 | 0.02 | 0.09 | 0.02 | 0.19 | 0.04 | 0.05 | 0.03 | 0.20 | 0.02 | 0.18 | 0.02 | 0.05 | 0.01 | 0.11 | 0.01 | 0.01 | 0.01 | 0.09 | 0.00 | 0.00 | 0.03 | 0.07 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.11 | 0.03 | 0.23 | 0.07 | 0.10 | 0.03 | 0.04 | 0.01 | 0.06 | 0.03 | 0.14 | 0.03 | 0.02 | 0.01 | 0.00 | 0.00 | 0.09 | 0.02 | 0.01 | 0.00 | 0.02 | 0.02 | 0.02 | 0.00 | 0.06 | 0.02 |
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