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 |
| CA7 | ENSG00000168748 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.06 | 0.00 | 0.06 | 0.11 | 0.02 | 0.00 | 0.00 | 0.03 | 0.06 | 0.04 | 0.02 | 0.05 | 0.01 | 0.03 | 0.01 | 0.13 | 0.00 | 0.04 | 0.02 | 0.00 | 0.00 | 0.02 | 0.01 | 0.01 | 0.00 | 0.03 | 0.04 | 0.05 | 0.01 | 0.23 | 0.03 | 0.01 | 0.02 | 0.00 | 0.01 | 0.02 | 0.05 | 0.05 | 0.29 | 0.03 | 0.04 | 0.03 | 0.07 | 0.05 | 0.14 | 0.03 | 0.04 | 0.15 | 0.01 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.00 | 0.03 | 0.04 | 0.01 |
| CELA2B | ENSG00000215704 | 0.00 | 0.06 | 0.01 | 0.08 | 0.00 | 0.00 | 0.01 | 0.03 | 0.09 | 0.08 | 0.00 | 0.03 | 0.04 | 0.26 | 0.06 | 0.06 | 0.06 | 0.11 | 0.04 | 0.10 | 0.12 | 0.09 | 0.08 | 0.08 | 0.01 | 0.15 | 0.00 | 0.21 | 0.02 | 0.06 | 0.02 | 0.21 | 0.00 | 1.11 | 0.01 | 0.11 | 0.01 | 0.09 | 0.00 | 0.00 | 0.02 | 0.20 | 0.17 | 0.38 | 0.06 | 0.08 | 0.10 | 0.11 | 0.04 | 0.25 | 0.19 | 0.17 | 0.05 | 0.09 | 0.02 | 0.00 | 0.00 | 0.07 | 0.00 | 0.02 | 0.05 | 0.09 | 0.00 | 0.07 | 0.07 | 0.09 |
| MAP3K19 | ENSG00000176601 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.18 | 0.06 | 0.03 | 0.00 | 0.01 | 0.00 | 0.00 | 0.03 | 0.01 | 0.06 | 0.03 | 0.04 | 0.01 | 0.08 | 0.07 | 0.04 | 0.06 | 0.00 | 0.02 | 0.02 | 0.01 | 0.01 | 0.01 | 0.02 | 0.04 | 0.05 | 0.03 | 0.05 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.06 | 0.10 | 0.16 | 0.04 | 0.01 | 0.02 | 0.02 | 0.09 | 0.00 | 0.09 | 0.04 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.13 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 |
| CACNA1F | ENSG00000102001 | 0.01 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.02 | 0.00 | 0.04 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.11 | 0.01 | 0.04 | 0.02 | 0.01 | 0.03 | 0.04 | 0.04 | 0.04 | 0.01 | 0.01 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.17 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.06 | 0.01 | 0.50 | 0.06 | 0.03 | 0.03 | 0.11 | 0.01 | 0.19 | 0.03 | 0.11 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.07 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.02 | 0.00 |
| HTR4 | ENSG00000164270 | 0.30 | 0.00 | 0.03 | 0.01 | 0.03 | 0.00 | 0.03 | 0.02 | 0.02 | 0.05 | 0.00 | 0.00 | 0.02 | 0.07 | 0.05 | 0.04 | 0.01 | 0.03 | 0.01 | 0.05 | 0.04 | 0.03 | 0.03 | 0.05 | 0.01 | 0.02 | 0.03 | 0.01 | 0.02 | 0.02 | 0.09 | 0.02 | 0.09 | 0.01 | 0.24 | 0.04 | 0.00 | 0.05 | 0.01 | 0.00 | 0.03 | 0.02 | 0.17 | 0.10 | 0.02 | 0.01 | 0.02 | 0.03 | 0.09 | 0.02 | 0.07 | 0.05 | 0.00 | 0.00 | 0.00 | 0.10 | 0.04 | 0.00 | 0.00 | 0.06 | 0.01 | 0.03 | 0.00 | 0.03 | 0.03 | 0.14 |
| WNT8A | ENSG00000061492 | 0.28 | 0.00 | 0.03 | 0.01 | 0.00 | 0.00 | 0.03 | 0.03 | 0.03 | 0.03 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.04 | 0.02 | 0.03 | 0.01 | 0.03 | 0.03 | 0.03 | 0.01 | 0.05 | 0.01 | 0.02 | 0.02 | 0.02 | 0.01 | 0.01 | 0.09 | 0.02 | 0.09 | 0.01 | 0.24 | 0.02 | 0.00 | 0.06 | 0.01 | 0.00 | 0.03 | 0.02 | 0.12 | 0.12 | 0.03 | 0.01 | 0.03 | 0.01 | 0.19 | 0.01 | 0.07 | 0.04 | 0.00 | 0.00 | 0.00 | 0.10 | 0.04 | 0.00 | 0.01 | 0.04 | 0.01 | 0.02 | 0.00 | 0.03 | 0.03 | 0.12 |
| IMPG2 | ENSG00000081148 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.04 | 0.02 | 0.00 | 0.00 | 0.00 | 0.05 | 0.05 | 0.02 | 0.15 | 0.02 | 0.06 | 0.01 | 0.09 | 0.04 | 0.06 | 0.02 | 0.00 | 0.01 | 0.03 | 0.02 | 0.00 | 0.01 | 0.02 | 0.01 | 0.00 | 0.10 | 0.11 | 0.01 | 0.00 | 0.06 | 0.00 | 0.00 | 0.06 | 0.02 | 0.21 | 0.04 | 0.07 | 0.02 | 0.04 | 0.01 | 0.22 | 0.08 | 0.11 | 0.05 | 0.04 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.03 | 0.01 | 0.03 | 0.00 | 0.00 | 0.03 | 0.01 |
| PDE6C | ENSG00000095464 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.12 | 0.04 | 0.10 | 0.00 | 0.02 | 0.00 | 0.14 | 0.01 | 0.03 | 0.04 | 0.07 | 0.01 | 0.05 | 0.02 | 0.08 | 0.00 | 0.10 | 0.01 | 0.09 | 0.00 | 0.07 | 0.01 | 0.05 | 0.01 | 0.06 | 0.16 | 0.07 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.01 | 0.02 | 0.08 | 0.09 | 0.31 | 0.00 | 0.06 | 0.04 | 0.10 | 0.09 | 0.09 | 0.01 | 0.06 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.07 | 0.01 | 0.03 | 0.00 | 0.05 | 0.00 | 0.00 | 0.01 | 0.03 |
| PNLIPRP1 | ENSG00000187021 | 0.00 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.05 | 0.03 | 0.10 | 0.00 | 0.02 | 0.01 | 0.17 | 0.03 | 0.02 | 0.04 | 0.05 | 0.01 | 0.03 | 0.04 | 0.06 | 0.07 | 0.06 | 0.01 | 0.06 | 0.01 | 0.05 | 0.01 | 0.01 | 0.02 | 0.10 | 0.14 | 0.25 | 0.12 | 0.00 | 0.01 | 0.02 | 0.00 | 0.00 | 0.03 | 0.09 | 0.14 | 0.22 | 0.01 | 0.06 | 0.05 | 0.06 | 0.04 | 0.05 | 0.04 | 0.05 | 0.07 | 0.01 | 0.00 | 0.00 | 0.00 | 0.05 | 0.00 | 0.12 | 0.00 | 0.06 | 0.00 | 0.00 | 0.01 | 0.05 |
| IL17A | ENSG00000112115 | 0.00 | 0.00 | 0.03 | 0.02 | 0.00 | 0.00 | 0.01 | 0.01 | 0.10 | 0.04 | 0.00 | 0.00 | 0.00 | 0.05 | 0.08 | 0.01 | 0.22 | 0.03 | 0.08 | 0.02 | 0.29 | 0.03 | 0.16 | 0.01 | 0.02 | 0.01 | 0.11 | 0.02 | 0.01 | 0.01 | 0.09 | 0.00 | 0.00 | 0.01 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.11 | 0.02 | 0.17 | 0.06 | 0.09 | 0.03 | 0.05 | 0.01 | 0.17 | 0.03 | 0.11 | 0.03 | 0.02 | 0.00 | 0.00 | 0.00 | 0.09 | 0.02 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 | 0.00 | 0.04 | 0.02 |
| CHIA | ENSG00000134216 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.04 | 0.05 | 0.06 | 0.00 | 0.00 | 0.00 | 0.35 | 0.01 | 0.14 | 0.01 | 0.15 | 0.00 | 0.13 | 0.03 | 0.13 | 0.02 | 0.07 | 0.00 | 0.06 | 0.05 | 0.08 | 0.00 | 0.02 | 0.01 | 0.03 | 0.00 | 0.10 | 0.04 | 0.04 | 0.00 | 0.26 | 0.00 | 0.00 | 0.04 | 0.10 | 0.17 | 0.14 | 0.01 | 0.08 | 0.01 | 0.03 | 0.01 | 0.07 | 0.04 | 0.11 | 0.03 | 0.04 | 0.00 | 0.01 | 0.00 | 0.05 | 0.00 | 0.01 | 0.01 | 0.03 | 0.03 | 0.03 | 0.07 | 0.10 |
| GLIPR1L1 | ENSG00000173401 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.02 | 0.02 | 0.02 | 0.07 | 0.04 | 0.00 | 0.00 | 0.01 | 0.05 | 0.07 | 0.03 | 0.05 | 0.03 | 0.01 | 0.04 | 0.12 | 0.06 | 0.01 | 0.03 | 0.00 | 0.03 | 0.01 | 0.05 | 0.00 | 0.05 | 0.03 | 0.01 | 0.05 | 0.01 | 0.11 | 0.02 | 0.05 | 0.00 | 0.00 | 0.00 | 0.11 | 0.04 | 0.07 | 0.14 | 0.00 | 0.02 | 0.01 | 0.02 | 0.07 | 0.10 | 0.59 | 0.05 | 0.04 | 0.00 | 0.00 | 0.00 | 0.07 | 0.00 | 0.00 | 0.02 | 0.06 | 0.05 | 0.02 | 0.00 | 0.06 | 0.04 |
| OPTC | ENSG00000188770 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.05 | 0.06 | 0.02 | 0.00 | 0.10 | 0.00 | 0.14 | 0.00 | 0.11 | 0.01 | 0.05 | 0.00 | 0.17 | 0.06 | 0.06 | 0.01 | 0.04 | 0.00 | 0.12 | 0.01 | 0.00 | 0.00 | 0.19 | 0.01 | 0.18 | 0.02 | 0.04 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.27 | 0.00 | 0.34 | 0.07 | 0.06 | 0.00 | 0.11 | 0.01 | 0.17 | 0.00 | 0.10 | 0.12 | 0.05 | 0.00 | 0.01 | 0.00 | 0.26 | 0.02 | 0.08 | 0.01 | 0.27 | 0.00 | 0.09 | 0.00 | 0.19 | 0.01 |
| SMYD1 | ENSG00000115593 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.03 | 0.08 | 0.01 | 0.00 | 0.00 | 0.02 | 0.03 | 0.03 | 0.01 | 0.08 | 0.02 | 0.06 | 0.01 | 0.09 | 0.01 | 0.01 | 0.01 | 0.00 | 0.01 | 0.01 | 0.02 | 0.00 | 0.01 | 0.02 | 0.02 | 0.00 | 0.02 | 0.04 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.04 | 0.02 | 0.10 | 0.04 | 0.04 | 0.01 | 0.04 | 0.02 | 0.08 | 0.02 | 0.18 | 0.04 | 0.01 | 0.04 | 0.00 | 0.00 | 0.00 | 0.04 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 |
| BPI | ENSG00000101425 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.01 | 0.03 | 0.07 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.06 | 0.03 | 0.11 | 0.02 | 0.03 | 0.01 | 0.06 | 0.01 | 0.08 | 0.00 | 0.08 | 0.00 | 0.17 | 0.00 | 0.00 | 0.00 | 0.04 | 0.01 | 0.00 | 0.04 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.11 | 0.02 | 0.09 | 0.07 | 0.05 | 0.02 | 0.05 | 0.01 | 0.18 | 0.00 | 0.13 | 0.05 | 0.00 | 0.01 | 0.00 | 0.03 | 0.03 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.04 | 0.00 |
| MLNR | ENSG00000102539 | 0.02 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.38 | 0.05 | 0.31 | 0.00 | 0.00 | 0.00 | 0.14 | 0.02 | 0.06 | 0.02 | 0.12 | 0.01 | 0.13 | 0.09 | 0.07 | 0.12 | 0.04 | 0.10 | 0.02 | 0.10 | 0.04 | 0.01 | 0.02 | 0.00 | 0.28 | 0.00 | 0.09 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.14 | 0.03 | 0.25 | 0.00 | 0.21 | 0.00 | 0.05 | 0.03 | 0.22 | 0.00 | 0.55 | 0.02 | 0.02 | 0.00 | 0.00 | 0.03 | 0.12 | 0.01 | 0.08 | 0.00 | 0.16 | 0.00 | 0.00 | 0.02 | 0.04 |
| ADAM32 | ENSG00000197140 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.08 | 0.07 | 0.38 | 0.06 | 0.00 | 0.00 | 0.04 | 0.00 | 0.18 | 0.03 | 0.77 | 0.03 | 0.23 | 0.02 | 0.28 | 0.05 | 0.08 | 0.04 | 0.17 | 0.03 | 0.19 | 0.04 | 0.05 | 0.00 | 0.09 | 0.06 | 0.03 | 0.01 | 0.09 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.61 | 0.04 | 0.22 | 0.10 | 0.09 | 0.03 | 0.12 | 0.03 | 0.71 | 0.11 | 0.21 | 0.06 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.01 | 0.04 | 0.04 |
| CEACAM3 | ENSG00000170956 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.02 | 0.01 | 0.03 | 0.14 | 0.03 | 0.00 | 0.00 | 0.05 | 0.05 | 0.10 | 0.04 | 0.16 | 0.07 | 0.01 | 0.02 | 0.07 | 0.06 | 0.07 | 0.03 | 0.03 | 0.01 | 0.03 | 0.02 | 0.02 | 0.04 | 0.02 | 0.03 | 0.12 | 0.01 | 0.06 | 0.04 | 0.00 | 0.02 | 0.00 | 0.00 | 0.07 | 0.05 | 0.16 | 0.27 | 0.11 | 0.04 | 0.05 | 0.04 | 0.09 | 0.17 | 0.27 | 0.10 | 0.00 | 0.04 | 0.01 | 0.00 | 0.05 | 0.03 | 0.02 | 0.09 | 0.03 | 0.09 | 0.00 | 0.00 | 0.03 | 0.03 |
| LIPJ | ENSG00000204022 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.45 | 0.03 | 0.16 | 0.00 | 0.02 | 0.01 | 0.14 | 0.01 | 0.05 | 0.02 | 0.16 | 0.01 | 0.09 | 0.03 | 0.16 | 0.01 | 0.14 | 0.01 | 0.11 | 0.00 | 0.09 | 0.01 | 0.04 | 0.01 | 0.10 | 0.20 | 0.07 | 0.02 | 0.01 | 0.00 | 0.03 | 0.00 | 0.01 | 0.02 | 0.15 | 0.07 | 0.31 | 0.02 | 0.13 | 0.04 | 0.14 | 0.06 | 0.12 | 0.01 | 0.20 | 0.01 | 0.04 | 0.00 | 0.01 | 0.00 | 0.16 | 0.00 | 0.06 | 0.00 | 0.28 | 0.00 | 0.00 | 0.00 | 0.14 |
| LIPI | ENSG00000188992 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.03 | 0.10 | 0.06 | 0.00 | 0.00 | 0.00 | 0.03 | 0.06 | 0.10 | 0.12 | 0.09 | 0.09 | 0.04 | 0.04 | 0.14 | 0.03 | 0.13 | 0.01 | 0.07 | 0.03 | 0.15 | 0.00 | 0.04 | 0.02 | 0.02 | 0.00 | 0.02 | 0.10 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.09 | 0.11 | 0.15 | 0.14 | 0.05 | 0.06 | 0.04 | 0.03 | 0.14 | 0.17 | 0.15 | 0.11 | 0.02 | 0.00 | 0.06 | 0.01 | 0.00 | 0.00 | 0.01 | 0.03 | 0.02 | 0.04 | 0.00 | 0.00 | 0.03 | 0.03 |
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