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 |
| LRP1 | ENSG00000123384 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.06 | 0.03 | 0.00 | 0.00 | 0.02 | 0.02 | 0.13 | 0.01 | 0.03 | 0.01 | 0.03 | 0.02 | 0.12 | 0.04 | 0.13 | 0.02 | 0.01 | 0.00 | 0.02 | 0.01 | 0.02 | 0.01 | 0.06 | 0.01 | 0.06 | 0.01 | 0.19 | 0.03 | 0.07 | 0.00 | 0.00 | 0.00 | 0.05 | 0.04 | 0.15 | 0.04 | 0.05 | 0.00 | 0.04 | 0.01 | 0.14 | 0.06 | 0.31 | 0.07 | 0.01 | 0.00 | 0.00 | 0.00 | 0.12 | 0.00 | 0.07 | 0.02 | 0.13 | 0.05 | 0.00 | 0.00 | 0.12 | 0.03 |
| AHR | ENSG00000106546 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.02 | 0.31 | 0.01 | 0.00 | 0.00 | 0.08 | 0.00 | 0.12 | 0.01 | 0.11 | 0.01 | 0.07 | 0.01 | 0.17 | 0.02 | 0.09 | 0.01 | 0.05 | 0.00 | 0.03 | 0.00 | 0.01 | 0.00 | 0.05 | 0.00 | 0.00 | 0.01 | 0.16 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.08 | 0.03 | 0.12 | 0.29 | 0.02 | 0.01 | 0.08 | 0.03 | 0.08 | 0.06 | 0.15 | 0.03 | 0.08 | 0.00 | 0.00 | 0.02 | 0.03 | 0.11 | 0.00 | 0.01 | 0.04 | 0.01 | 0.00 | 0.00 | 0.12 | 0.02 |
| MATK | ENSG00000007264 | 0.00 | 0.01 | 0.00 | 0.02 | 0.00 | 0.04 | 0.00 | 0.05 | 0.03 | 0.13 | 0.02 | 0.00 | 0.01 | 0.10 | 0.01 | 0.09 | 0.02 | 0.12 | 0.03 | 0.11 | 0.09 | 0.11 | 0.00 | 0.09 | 0.01 | 0.05 | 0.01 | 0.10 | 0.01 | 0.06 | 0.02 | 0.14 | 0.00 | 0.03 | 0.04 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.05 | 0.11 | 0.03 | 0.87 | 0.04 | 0.19 | 0.00 | 0.28 | 0.04 | 0.74 | 0.17 | 0.08 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.03 | 0.02 | 0.02 | 0.04 | 0.01 | 0.00 | 0.05 | 0.03 | 0.06 |
| PVRL2 | ENSG00000130202 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.03 | 0.14 | 0.02 | 0.00 | 0.00 | 0.05 | 0.05 | 0.14 | 0.05 | 0.13 | 0.08 | 0.07 | 0.02 | 0.10 | 0.05 | 0.15 | 0.01 | 0.01 | 0.02 | 0.01 | 0.02 | 0.09 | 0.02 | 0.07 | 0.04 | 0.12 | 0.03 | 0.24 | 0.03 | 0.00 | 0.02 | 0.00 | 0.00 | 0.08 | 0.05 | 0.20 | 0.30 | 0.21 | 0.03 | 0.13 | 0.04 | 0.31 | 0.17 | 0.08 | 0.16 | 0.00 | 0.04 | 0.01 | 0.00 | 0.07 | 0.03 | 0.02 | 0.12 | 0.02 | 0.09 | 0.00 | 0.00 | 0.02 | 0.02 |
| CR1L | ENSG00000197721 | 0.02 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.03 | 0.06 | 0.06 | 0.01 | 0.00 | 0.07 | 0.01 | 0.12 | 0.01 | 0.09 | 0.01 | 0.05 | 0.00 | 0.15 | 0.06 | 0.06 | 0.02 | 0.04 | 0.00 | 0.13 | 0.02 | 0.00 | 0.00 | 0.16 | 0.01 | 0.18 | 0.02 | 0.01 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.26 | 0.01 | 0.20 | 0.12 | 0.06 | 0.00 | 0.06 | 0.02 | 0.13 | 0.04 | 0.06 | 0.18 | 0.02 | 0.03 | 0.01 | 0.00 | 0.16 | 0.13 | 0.00 | 0.02 | 0.03 | 0.02 | 0.09 | 0.00 | 0.14 | 0.02 |
| KDM1B | ENSG00000165097 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 | 0.52 | 0.04 | 0.00 | 0.01 | 0.01 | 0.04 | 0.06 | 0.01 | 0.11 | 0.06 | 0.04 | 0.05 | 0.10 | 0.16 | 0.06 | 0.07 | 0.03 | 0.03 | 0.02 | 0.03 | 0.02 | 0.06 | 0.13 | 0.02 | 0.06 | 0.03 | 0.02 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.16 | 0.03 | 0.54 | 0.04 | 0.10 | 0.06 | 0.11 | 0.02 | 0.37 | 0.02 | 0.05 | 0.13 | 0.02 | 0.02 | 0.00 | 0.00 | 0.05 | 0.01 | 0.01 | 0.02 | 0.03 | 0.01 | 0.27 | 0.00 | 0.19 | 0.00 |
| ADAMTS13 | ENSG00000160323 | 0.00 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.04 | 0.01 | 0.05 | 0.02 | 0.00 | 0.01 | 0.00 | 0.02 | 0.05 | 0.02 | 0.07 | 0.03 | 0.07 | 0.03 | 0.12 | 0.04 | 0.12 | 0.01 | 0.02 | 0.01 | 0.05 | 0.03 | 0.01 | 0.00 | 0.05 | 0.03 | 0.06 | 0.01 | 0.12 | 0.04 | 0.00 | 0.01 | 0.00 | 0.00 | 0.05 | 0.06 | 0.07 | 0.25 | 0.07 | 0.01 | 0.03 | 0.06 | 0.04 | 0.14 | 0.07 | 0.14 | 0.03 | 0.03 | 0.01 | 0.00 | 0.05 | 0.00 | 0.02 | 0.01 | 0.03 | 0.03 | 0.00 | 0.00 | 0.02 | 0.02 |
| HSPB1 | ENSG00000106211 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.05 | 0.02 | 0.00 | 0.00 | 0.02 | 0.00 | 0.04 | 0.02 | 0.11 | 0.02 | 0.05 | 0.03 | 0.16 | 0.02 | 0.12 | 0.01 | 0.01 | 0.00 | 0.02 | 0.00 | 0.02 | 0.01 | 0.05 | 0.01 | 0.00 | 0.01 | 0.12 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.06 | 0.02 | 0.17 | 0.07 | 0.04 | 0.01 | 0.07 | 0.02 | 0.10 | 0.03 | 0.05 | 0.07 | 0.09 | 0.00 | 0.00 | 0.00 | 0.10 | 0.00 | 0.02 | 0.01 | 0.06 | 0.00 | 0.00 | 0.00 | 0.06 | 0.02 |
| MAP3K12 | ENSG00000139625 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.02 | 0.00 | 0.04 | 0.03 | 0.00 | 0.00 | 0.00 | 0.04 | 0.06 | 0.01 | 0.04 | 0.02 | 0.01 | 0.03 | 0.06 | 0.05 | 0.06 | 0.04 | 0.02 | 0.00 | 0.03 | 0.01 | 0.01 | 0.02 | 0.02 | 0.01 | 0.17 | 0.01 | 0.14 | 0.00 | 0.03 | 0.01 | 0.00 | 0.00 | 0.04 | 0.06 | 0.09 | 0.06 | 0.03 | 0.00 | 0.07 | 0.01 | 0.39 | 0.06 | 0.11 | 0.09 | 0.00 | 0.00 | 0.00 | 0.00 | 0.12 | 0.00 | 0.00 | 0.04 | 0.02 | 0.04 | 0.00 | 0.00 | 0.03 | 0.06 |
| CEACAM7 | ENSG00000007306 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.02 | 0.01 | 0.04 | 0.16 | 0.03 | 0.00 | 0.00 | 0.05 | 0.05 | 0.10 | 0.04 | 0.15 | 0.07 | 0.02 | 0.02 | 0.06 | 0.06 | 0.06 | 0.03 | 0.03 | 0.01 | 0.03 | 0.02 | 0.03 | 0.04 | 0.02 | 0.03 | 0.12 | 0.01 | 0.06 | 0.04 | 0.00 | 0.02 | 0.00 | 0.00 | 0.06 | 0.05 | 0.17 | 0.27 | 0.11 | 0.04 | 0.06 | 0.04 | 0.09 | 0.17 | 0.25 | 0.10 | 0.00 | 0.04 | 0.01 | 0.00 | 0.05 | 0.03 | 0.02 | 0.09 | 0.02 | 0.09 | 0.00 | 0.00 | 0.03 | 0.03 |
| VWA2 | ENSG00000165816 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.05 | 0.02 | 0.09 | 0.00 | 0.02 | 0.01 | 0.17 | 0.06 | 0.03 | 0.04 | 0.06 | 0.01 | 0.03 | 0.03 | 0.07 | 0.07 | 0.06 | 0.01 | 0.06 | 0.01 | 0.06 | 0.01 | 0.01 | 0.01 | 0.10 | 0.11 | 0.25 | 0.09 | 0.00 | 0.01 | 0.02 | 0.00 | 0.00 | 0.04 | 0.10 | 0.19 | 0.22 | 0.01 | 0.06 | 0.03 | 0.06 | 0.04 | 0.05 | 0.04 | 0.06 | 0.07 | 0.00 | 0.00 | 0.00 | 0.00 | 0.10 | 0.00 | 0.11 | 0.00 | 0.06 | 0.00 | 0.00 | 0.01 | 0.05 |
| LPAR3 | ENSG00000171517 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.07 | 0.05 | 0.07 | 0.00 | 0.00 | 0.00 | 0.28 | 0.05 | 0.08 | 0.04 | 0.05 | 0.01 | 0.07 | 0.01 | 0.07 | 0.01 | 0.06 | 0.00 | 0.07 | 0.01 | 0.07 | 0.00 | 0.01 | 0.02 | 0.03 | 0.00 | 0.08 | 0.04 | 0.04 | 0.00 | 0.20 | 0.00 | 0.00 | 0.05 | 0.09 | 0.11 | 0.21 | 0.02 | 0.04 | 0.02 | 0.03 | 0.13 | 0.05 | 0.14 | 0.06 | 0.03 | 0.05 | 0.01 | 0.02 | 0.10 | 0.00 | 0.01 | 0.01 | 0.02 | 0.04 | 0.03 | 0.03 | 0.05 | 0.10 |
| HPRT1 | ENSG00000165704 | 0.02 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.10 | 0.03 | 0.05 | 0.00 | 0.06 | 0.01 | 0.13 | 0.02 | 0.09 | 0.02 | 0.06 | 0.01 | 0.13 | 0.01 | 0.15 | 0.01 | 0.03 | 0.00 | 0.07 | 0.01 | 0.04 | 0.00 | 0.08 | 0.03 | 0.00 | 0.01 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.02 | 0.27 | 0.05 | 0.12 | 0.00 | 0.03 | 0.01 | 0.04 | 0.10 | 0.04 | 0.13 | 0.00 | 0.02 | 0.00 | 0.01 | 0.06 | 0.05 | 0.01 | 0.02 | 0.01 | 0.01 | 0.00 | 0.00 | 0.03 | 0.00 |
| STK24 | ENSG00000102572 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.04 | 0.02 | 0.05 | 0.18 | 0.03 | 0.00 | 0.01 | 0.01 | 0.01 | 0.11 | 0.03 | 0.09 | 0.06 | 0.08 | 0.02 | 0.08 | 0.08 | 0.15 | 0.04 | 0.09 | 0.01 | 0.15 | 0.01 | 0.02 | 0.02 | 0.27 | 0.04 | 0.06 | 0.01 | 0.03 | 0.03 | 0.01 | 0.00 | 0.00 | 0.00 | 0.14 | 0.05 | 0.24 | 0.10 | 0.18 | 0.03 | 0.06 | 0.02 | 0.35 | 0.11 | 0.22 | 0.14 | 0.01 | 0.01 | 0.00 | 0.00 | 0.04 | 0.04 | 0.03 | 0.02 | 0.03 | 0.04 | 0.05 | 0.00 | 0.07 | 0.06 |
| ABCC8 | ENSG00000006071 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.05 | 0.01 | 0.01 | 0.01 | 0.08 | 0.00 | 0.00 | 0.02 | 0.03 | 0.03 | 0.04 | 0.07 | 0.07 | 0.01 | 0.04 | 0.05 | 0.03 | 0.03 | 0.02 | 0.02 | 0.00 | 0.02 | 0.01 | 0.02 | 0.03 | 0.04 | 0.01 | 0.03 | 0.01 | 0.00 | 0.02 | 0.06 | 0.05 | 0.00 | 0.00 | 0.07 | 0.05 | 0.04 | 0.25 | 0.01 | 0.06 | 0.03 | 0.04 | 0.01 | 0.04 | 0.08 | 0.08 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.03 | 0.00 | 0.01 | 0.00 | 0.00 | 0.03 | 0.01 |
| SLC29A2 | ENSG00000174669 | 0.01 | 0.00 | 0.00 | 0.01 | 0.09 | 0.00 | 0.07 | 0.00 | 0.16 | 0.01 | 0.00 | 0.00 | 0.08 | 0.00 | 0.11 | 0.01 | 0.13 | 0.01 | 0.34 | 0.01 | 0.25 | 0.01 | 0.08 | 0.03 | 0.01 | 0.02 | 0.02 | 0.03 | 0.02 | 0.02 | 0.07 | 0.02 | 0.00 | 0.05 | 0.03 | 0.01 | 0.03 | 0.00 | 0.00 | 0.00 | 0.26 | 0.04 | 0.24 | 0.03 | 0.13 | 0.00 | 0.11 | 0.02 | 0.22 | 0.06 | 0.13 | 0.03 | 0.01 | 0.05 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.01 | 0.01 | 0.02 | 0.00 | 0.00 | 0.13 | 0.03 |
| HTR7 | ENSG00000148680 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.15 | 0.03 | 0.09 | 0.00 | 0.02 | 0.01 | 0.12 | 0.02 | 0.03 | 0.02 | 0.07 | 0.01 | 0.05 | 0.02 | 0.08 | 0.01 | 0.09 | 0.00 | 0.09 | 0.00 | 0.08 | 0.01 | 0.02 | 0.01 | 0.06 | 0.16 | 0.07 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.09 | 0.06 | 0.30 | 0.01 | 0.06 | 0.04 | 0.09 | 0.03 | 0.13 | 0.01 | 0.04 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.09 | 0.00 | 0.03 | 0.01 | 0.04 | 0.00 | 0.03 | 0.00 | 0.04 |
| FAS | ENSG00000026103 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.25 | 0.04 | 0.13 | 0.00 | 0.02 | 0.01 | 0.14 | 0.01 | 0.05 | 0.02 | 0.12 | 0.01 | 0.09 | 0.02 | 0.13 | 0.00 | 0.13 | 0.01 | 0.09 | 0.00 | 0.08 | 0.01 | 0.02 | 0.01 | 0.08 | 0.20 | 0.07 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.02 | 0.01 | 0.11 | 0.07 | 0.31 | 0.01 | 0.12 | 0.04 | 0.12 | 0.09 | 0.12 | 0.01 | 0.14 | 0.01 | 0.00 | 0.00 | 0.02 | 0.00 | 0.24 | 0.00 | 0.04 | 0.00 | 0.14 | 0.00 | 0.00 | 0.00 | 0.05 |
| BRWD3 | ENSG00000165288 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.01 | 0.02 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.02 | 0.07 | 0.03 | 0.03 | 0.01 | 0.07 | 0.06 | 0.03 | 0.01 | 0.02 | 0.01 | 0.00 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.07 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.02 | 0.10 | 0.04 | 0.01 | 0.02 | 0.03 | 0.02 | 0.03 | 0.00 | 0.15 | 0.11 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.06 | 0.02 | 0.00 | 0.01 | 0.01 | 0.00 | 0.02 | 0.03 | 0.01 |
| FGA | ENSG00000171560 | 0.01 | 0.02 | 0.00 | 0.01 | 0.06 | 0.00 | 0.01 | 0.02 | 0.05 | 0.11 | 0.00 | 0.02 | 0.00 | 0.01 | 0.05 | 0.06 | 0.01 | 0.11 | 0.02 | 0.09 | 0.05 | 0.06 | 0.05 | 0.07 | 0.01 | 0.06 | 0.02 | 0.04 | 0.01 | 0.04 | 0.09 | 0.06 | 0.00 | 0.12 | 0.10 | 0.05 | 0.00 | 0.03 | 0.00 | 0.00 | 0.06 | 0.07 | 0.07 | 0.26 | 0.03 | 0.08 | 0.04 | 0.05 | 0.06 | 0.05 | 0.10 | 0.10 | 0.01 | 0.01 | 0.00 | 0.00 | 0.03 | 0.03 | 0.00 | 0.09 | 0.00 | 0.03 | 0.00 | 0.00 | 0.04 | 0.05 |
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