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 |
| TMPRSS11D | ENSG00000153802 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.04 | 0.10 | 0.02 | 0.00 | 0.00 | 0.00 | 0.07 | 0.05 | 0.02 | 0.19 | 0.01 | 0.08 | 0.01 | 0.12 | 0.01 | 0.03 | 0.02 | 0.01 | 0.01 | 0.03 | 0.01 | 0.00 | 0.01 | 0.02 | 0.07 | 0.00 | 0.03 | 0.06 | 0.00 | 0.04 | 0.02 | 0.00 | 0.00 | 0.08 | 0.02 | 0.20 | 0.08 | 0.05 | 0.04 | 0.04 | 0.02 | 0.02 | 0.05 | 0.10 | 0.06 | 0.10 | 0.01 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.02 | 0.00 | 0.03 | 0.00 | 0.00 | 0.02 | 0.04 |
| MARK3 | ENSG00000075413 | 0.00 | 0.02 | 0.01 | 0.02 | 0.00 | 0.04 | 0.02 | 0.03 | 0.07 | 0.08 | 0.00 | 0.00 | 0.00 | 0.09 | 0.06 | 0.06 | 0.20 | 0.03 | 0.06 | 0.05 | 0.08 | 0.07 | 0.04 | 0.07 | 0.00 | 0.03 | 0.03 | 0.03 | 0.02 | 0.03 | 0.02 | 0.13 | 0.00 | 0.31 | 0.15 | 0.00 | 0.01 | 0.04 | 0.00 | 0.00 | 0.09 | 0.08 | 0.32 | 0.17 | 0.07 | 0.09 | 0.09 | 0.02 | 0.20 | 0.02 | 0.21 | 0.05 | 0.03 | 0.01 | 0.00 | 0.00 | 0.00 | 0.07 | 0.01 | 0.07 | 0.03 | 0.05 | 0.03 | 0.03 | 0.01 | 0.06 |
| ATP2B3 | ENSG00000067842 | 0.03 | 0.01 | 0.02 | 0.00 | 0.01 | 0.00 | 0.02 | 0.00 | 0.11 | 0.04 | 0.06 | 0.00 | 0.06 | 0.01 | 0.23 | 0.01 | 0.18 | 0.02 | 0.14 | 0.01 | 0.23 | 0.01 | 0.17 | 0.02 | 0.05 | 0.00 | 0.10 | 0.01 | 0.07 | 0.00 | 0.12 | 0.03 | 0.10 | 0.01 | 0.25 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.10 | 0.02 | 0.43 | 0.09 | 0.22 | 0.02 | 0.10 | 0.03 | 0.17 | 0.07 | 0.24 | 0.07 | 0.01 | 0.02 | 0.00 | 0.00 | 0.15 | 0.07 | 0.02 | 0.03 | 0.03 | 0.01 | 0.05 | 0.00 | 0.06 | 0.04 |
| ADGRG1 | ENSG00000205336 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.01 | 0.04 | 0.00 | 0.00 | 0.00 | 0.01 | 0.05 | 0.03 | 0.04 | 0.01 | 0.03 | 0.02 | 0.10 | 0.01 | 0.03 | 0.04 | 0.02 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.03 | 0.02 | 0.00 | 0.01 | 0.06 | 0.06 | 0.00 | 0.02 | 0.00 | 0.00 | 0.04 | 0.04 | 0.05 | 0.14 | 0.00 | 0.07 | 0.04 | 0.07 | 0.03 | 0.16 | 0.02 | 0.05 | 0.12 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.01 | 0.01 | 0.02 | 0.00 | 0.03 | 0.02 | 0.04 |
| MAP3K5 | ENSG00000197442 | 0.00 | 0.05 | 0.00 | 0.01 | 0.00 | 0.05 | 0.01 | 0.02 | 0.10 | 0.06 | 0.00 | 0.01 | 0.00 | 0.14 | 0.04 | 0.05 | 0.06 | 0.04 | 0.07 | 0.02 | 0.14 | 0.01 | 0.11 | 0.02 | 0.02 | 0.01 | 0.04 | 0.02 | 0.03 | 0.02 | 0.01 | 0.09 | 0.00 | 0.10 | 0.21 | 0.02 | 0.01 | 0.02 | 0.00 | 0.00 | 0.10 | 0.06 | 0.08 | 0.29 | 0.02 | 0.05 | 0.05 | 0.02 | 0.08 | 0.05 | 0.39 | 0.03 | 0.01 | 0.04 | 0.00 | 0.00 | 0.00 | 0.25 | 0.00 | 0.05 | 0.01 | 0.12 | 0.05 | 0.09 | 0.02 | 0.14 |
| CA3 | ENSG00000164879 | 0.01 | 0.00 | 0.00 | 0.01 | 0.06 | 0.00 | 0.07 | 0.01 | 0.17 | 0.01 | 0.00 | 0.00 | 0.02 | 0.00 | 0.16 | 0.02 | 0.13 | 0.02 | 0.06 | 0.01 | 0.17 | 0.00 | 0.12 | 0.01 | 0.09 | 0.00 | 0.13 | 0.03 | 0.02 | 0.02 | 0.15 | 0.00 | 0.20 | 0.01 | 0.06 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.27 | 0.01 | 0.27 | 0.12 | 0.05 | 0.01 | 0.06 | 0.01 | 0.21 | 0.02 | 0.21 | 0.05 | 0.17 | 0.00 | 0.00 | 0.00 | 0.04 | 0.02 | 0.02 | 0.00 | 0.01 | 0.01 | 0.22 | 0.00 | 0.10 | 0.01 |
| ABCA3 | ENSG00000167972 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.01 | 0.15 | 0.00 | 0.00 | 0.04 | 0.02 | 0.04 | 0.04 | 0.03 | 0.08 | 0.03 | 0.03 | 0.02 | 0.10 | 0.02 | 0.08 | 0.03 | 0.03 | 0.01 | 0.03 | 0.01 | 0.02 | 0.04 | 0.03 | 0.00 | 0.05 | 0.17 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.10 | 0.02 | 0.10 | 0.17 | 0.11 | 0.04 | 0.06 | 0.03 | 0.15 | 0.05 | 0.10 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.09 | 0.00 | 0.01 | 0.00 | 0.03 | 0.02 | 0.00 | 0.00 | 0.04 | 0.02 |
| TDRD12 | ENSG00000173809 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.02 | 0.01 | 0.00 | 0.26 | 0.03 | 0.00 | 0.00 | 0.11 | 0.01 | 0.25 | 0.01 | 0.37 | 0.02 | 0.06 | 0.02 | 0.22 | 0.03 | 0.14 | 0.06 | 0.07 | 0.00 | 0.04 | 0.00 | 0.12 | 0.00 | 0.04 | 0.03 | 0.13 | 0.03 | 0.00 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.14 | 0.01 | 0.68 | 0.04 | 0.14 | 0.01 | 0.23 | 0.02 | 1.62 | 0.01 | 0.29 | 0.03 | 0.01 | 0.00 | 0.00 | 0.00 | 0.13 | 0.00 | 0.01 | 0.00 | 0.03 | 0.03 | 0.00 | 0.00 | 0.05 | 0.02 |
| KCNK1 | ENSG00000135750 | 0.01 | 0.02 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.10 | 0.12 | 0.04 | 0.02 | 0.00 | 0.05 | 0.05 | 0.09 | 0.01 | 0.12 | 0.02 | 0.06 | 0.00 | 0.21 | 0.03 | 0.11 | 0.02 | 0.03 | 0.02 | 0.05 | 0.06 | 0.01 | 0.01 | 0.17 | 0.01 | 0.23 | 0.02 | 0.04 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.25 | 0.02 | 0.47 | 0.08 | 0.09 | 0.02 | 0.09 | 0.02 | 0.28 | 0.00 | 0.02 | 0.24 | 0.04 | 0.04 | 0.02 | 0.00 | 0.02 | 0.15 | 0.00 | 0.03 | 0.02 | 0.04 | 0.09 | 0.03 | 0.15 | 0.04 |
| MAPKAPK3 | ENSG00000114738 | 0.00 | 0.17 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.02 | 0.03 | 0.16 | 0.00 | 0.02 | 0.00 | 0.54 | 0.01 | 0.06 | 0.00 | 0.11 | 0.00 | 0.06 | 0.01 | 0.14 | 0.01 | 0.11 | 0.00 | 0.05 | 0.01 | 0.08 | 0.00 | 0.05 | 0.04 | 0.06 | 0.00 | 0.20 | 0.01 | 0.02 | 0.00 | 0.04 | 0.00 | 0.00 | 0.01 | 0.17 | 0.04 | 0.20 | 0.00 | 0.06 | 0.06 | 0.07 | 0.09 | 0.29 | 0.03 | 0.17 | 0.02 | 0.01 | 0.00 | 0.01 | 0.00 | 0.06 | 0.01 | 0.06 | 0.01 | 0.04 | 0.00 | 0.03 | 0.02 | 0.04 |
| MYSM1 | ENSG00000162601 | 0.00 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.07 | 0.09 | 0.05 | 0.00 | 0.00 | 0.04 | 0.03 | 0.07 | 0.06 | 0.07 | 0.04 | 0.06 | 0.03 | 0.06 | 0.05 | 0.02 | 0.05 | 0.00 | 0.05 | 0.00 | 0.04 | 0.00 | 0.01 | 0.03 | 0.04 | 0.00 | 0.17 | 0.04 | 0.03 | 0.00 | 0.18 | 0.00 | 0.00 | 0.08 | 0.06 | 0.26 | 0.14 | 0.14 | 0.02 | 0.03 | 0.02 | 0.05 | 0.06 | 0.61 | 0.02 | 0.04 | 0.03 | 0.02 | 0.00 | 0.00 | 0.03 | 0.00 | 0.01 | 0.02 | 0.01 | 0.00 | 0.07 | 0.02 | 0.03 |
| SMOC2 | ENSG00000112562 | 0.00 | 0.05 | 0.00 | 0.02 | 0.00 | 0.05 | 0.00 | 0.06 | 0.04 | 0.12 | 0.00 | 0.01 | 0.04 | 0.09 | 0.02 | 0.07 | 0.09 | 0.07 | 0.04 | 0.04 | 0.12 | 0.05 | 0.10 | 0.08 | 0.02 | 0.03 | 0.03 | 0.03 | 0.00 | 0.03 | 0.02 | 0.14 | 0.06 | 0.21 | 0.11 | 0.08 | 0.00 | 0.04 | 0.01 | 0.00 | 0.06 | 0.15 | 0.09 | 0.47 | 0.02 | 0.11 | 0.08 | 0.05 | 0.25 | 0.10 | 0.21 | 0.09 | 0.01 | 0.05 | 0.00 | 0.00 | 0.03 | 0.08 | 0.00 | 0.05 | 0.01 | 0.13 | 0.05 | 0.06 | 0.02 | 0.17 |
| GRID2 | ENSG00000152208 | 0.01 | 0.01 | 0.02 | 0.00 | 0.00 | 0.00 | 0.02 | 0.03 | 0.06 | 0.08 | 0.00 | 0.00 | 0.00 | 0.07 | 0.02 | 0.03 | 0.07 | 0.06 | 0.03 | 0.04 | 0.03 | 0.10 | 0.02 | 0.08 | 0.01 | 0.02 | 0.00 | 0.01 | 0.00 | 0.01 | 0.01 | 0.12 | 0.00 | 0.06 | 0.07 | 0.02 | 0.05 | 0.04 | 0.00 | 0.00 | 0.05 | 0.05 | 0.04 | 0.28 | 0.01 | 0.05 | 0.02 | 0.07 | 0.21 | 0.16 | 0.06 | 0.09 | 0.01 | 0.23 | 0.00 | 0.00 | 0.00 | 0.05 | 0.01 | 0.02 | 0.02 | 0.03 | 0.00 | 0.00 | 0.02 | 0.05 |
| TNNT2 | ENSG00000118194 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.08 | 0.07 | 0.02 | 0.00 | 0.10 | 0.00 | 0.14 | 0.00 | 0.08 | 0.01 | 0.06 | 0.01 | 0.14 | 0.05 | 0.04 | 0.01 | 0.04 | 0.01 | 0.07 | 0.04 | 0.00 | 0.00 | 0.18 | 0.01 | 0.18 | 0.02 | 0.05 | 0.04 | 0.02 | 0.00 | 0.00 | 0.00 | 0.22 | 0.01 | 0.30 | 0.06 | 0.06 | 0.00 | 0.08 | 0.02 | 0.18 | 0.03 | 0.10 | 0.12 | 0.07 | 0.00 | 0.01 | 0.00 | 0.26 | 0.02 | 0.01 | 0.01 | 0.02 | 0.01 | 0.06 | 0.00 | 0.21 | 0.01 |
| ATXN3 | ENSG00000066427 | 0.00 | 0.02 | 0.01 | 0.01 | 0.00 | 0.04 | 0.01 | 0.06 | 0.05 | 0.06 | 0.00 | 0.00 | 0.00 | 0.05 | 0.05 | 0.05 | 0.11 | 0.02 | 0.04 | 0.05 | 0.08 | 0.06 | 0.03 | 0.04 | 0.00 | 0.03 | 0.01 | 0.02 | 0.02 | 0.01 | 0.01 | 0.09 | 0.00 | 0.31 | 0.05 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.04 | 0.09 | 0.19 | 0.17 | 0.07 | 0.09 | 0.04 | 0.03 | 0.06 | 0.02 | 0.06 | 0.08 | 0.03 | 0.01 | 0.00 | 0.00 | 0.03 | 0.00 | 0.00 | 0.10 | 0.02 | 0.06 | 0.03 | 0.01 | 0.01 | 0.06 |
| C5 | ENSG00000106804 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.02 | 0.02 | 0.04 | 0.00 | 0.01 | 0.01 | 0.01 | 0.05 | 0.02 | 0.06 | 0.02 | 0.05 | 0.01 | 0.11 | 0.03 | 0.08 | 0.01 | 0.01 | 0.01 | 0.05 | 0.02 | 0.00 | 0.01 | 0.04 | 0.04 | 0.06 | 0.04 | 0.08 | 0.02 | 0.03 | 0.00 | 0.00 | 0.00 | 0.06 | 0.04 | 0.10 | 0.13 | 0.02 | 0.01 | 0.02 | 0.04 | 0.00 | 0.15 | 0.06 | 0.05 | 0.03 | 0.02 | 0.00 | 0.00 | 0.05 | 0.00 | 0.01 | 0.01 | 0.04 | 0.02 | 0.00 | 0.00 | 0.02 | 0.02 |
| SMPDL3B | ENSG00000130768 | 0.00 | 0.06 | 0.00 | 0.08 | 0.00 | 0.00 | 0.01 | 0.03 | 0.04 | 0.09 | 0.00 | 0.01 | 0.05 | 0.19 | 0.04 | 0.06 | 0.03 | 0.09 | 0.03 | 0.06 | 0.04 | 0.13 | 0.01 | 0.12 | 0.00 | 0.16 | 0.00 | 0.21 | 0.00 | 0.09 | 0.00 | 0.21 | 0.00 | 1.02 | 0.00 | 0.04 | 0.01 | 0.08 | 0.00 | 0.00 | 0.02 | 0.17 | 0.10 | 0.43 | 0.04 | 0.08 | 0.03 | 0.13 | 0.04 | 0.18 | 0.12 | 0.09 | 0.04 | 0.04 | 0.02 | 0.00 | 0.00 | 0.07 | 0.00 | 0.01 | 0.02 | 0.07 | 0.00 | 0.07 | 0.07 | 0.05 |
| TPO | ENSG00000115705 | 0.00 | 0.00 | 0.01 | 0.02 | 0.00 | 0.06 | 0.02 | 0.01 | 0.15 | 0.03 | 0.00 | 0.00 | 0.03 | 0.04 | 0.07 | 0.03 | 0.12 | 0.07 | 0.03 | 0.04 | 0.05 | 0.07 | 0.03 | 0.04 | 0.02 | 0.02 | 0.04 | 0.04 | 0.01 | 0.04 | 0.11 | 0.01 | 0.00 | 0.05 | 0.01 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.07 | 0.04 | 0.29 | 0.18 | 0.09 | 0.02 | 0.11 | 0.04 | 0.30 | 0.08 | 0.04 | 0.19 | 0.14 | 0.02 | 0.00 | 0.00 | 0.02 | 0.08 | 0.03 | 0.03 | 0.02 | 0.05 | 0.05 | 0.00 | 0.02 | 0.04 |
| GPNMB | ENSG00000136235 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.10 | 0.01 | 0.00 | 0.00 | 0.03 | 0.00 | 0.10 | 0.01 | 0.15 | 0.01 | 0.05 | 0.01 | 0.20 | 0.01 | 0.08 | 0.01 | 0.05 | 0.00 | 0.03 | 0.00 | 0.02 | 0.00 | 0.06 | 0.00 | 0.00 | 0.01 | 0.06 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.12 | 0.02 | 0.18 | 0.19 | 0.05 | 0.00 | 0.08 | 0.03 | 0.45 | 0.01 | 0.14 | 0.04 | 0.06 | 0.00 | 0.00 | 0.01 | 0.19 | 0.02 | 0.02 | 0.00 | 0.05 | 0.01 | 0.00 | 0.00 | 0.08 | 0.02 |
| SLC4A10 | ENSG00000144290 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.10 | 0.13 | 0.03 | 0.00 | 0.01 | 0.00 | 0.01 | 0.07 | 0.01 | 0.10 | 0.03 | 0.05 | 0.02 | 0.10 | 0.03 | 0.03 | 0.04 | 0.01 | 0.02 | 0.01 | 0.02 | 0.05 | 0.01 | 0.04 | 0.06 | 0.00 | 0.05 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.03 | 0.32 | 0.04 | 0.05 | 0.01 | 0.06 | 0.01 | 0.03 | 0.02 | 0.09 | 0.08 | 0.03 | 0.01 | 0.00 | 0.00 | 0.00 | 0.15 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.03 | 0.02 |
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