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 |
| PTPN20 | ENSG00000204179 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.07 | 0.10 | 0.07 | 0.00 | 0.00 | 0.01 | 0.04 | 0.04 | 0.03 | 0.08 | 0.03 | 0.05 | 0.03 | 0.11 | 0.09 | 0.03 | 0.02 | 0.00 | 0.03 | 0.00 | 0.01 | 0.00 | 0.01 | 0.01 | 0.02 | 0.15 | 0.01 | 0.07 | 0.07 | 0.00 | 0.00 | 0.00 | 0.01 | 0.05 | 0.05 | 0.12 | 0.14 | 0.00 | 0.02 | 0.02 | 0.04 | 0.05 | 0.06 | 0.08 | 0.11 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.03 | 0.03 |
| HSD17B8 | ENSG00000204228 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.06 | 0.04 | 0.00 | 0.00 | 0.02 | 0.02 | 0.07 | 0.01 | 0.05 | 0.05 | 0.02 | 0.04 | 0.14 | 0.04 | 0.08 | 0.04 | 0.03 | 0.02 | 0.06 | 0.01 | 0.01 | 0.02 | 0.07 | 0.01 | 0.05 | 0.03 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.08 | 0.02 | 0.27 | 0.05 | 0.09 | 0.01 | 0.04 | 0.01 | 0.05 | 0.01 | 0.03 | 0.07 | 0.00 | 0.01 | 0.00 | 0.00 | 0.05 | 0.06 | 0.01 | 0.00 | 0.01 | 0.01 | 0.11 | 0.00 | 0.11 | 0.01 |
| RXRB | ENSG00000204231 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.06 | 0.04 | 0.00 | 0.00 | 0.02 | 0.02 | 0.07 | 0.01 | 0.05 | 0.05 | 0.02 | 0.04 | 0.14 | 0.04 | 0.08 | 0.04 | 0.03 | 0.02 | 0.06 | 0.01 | 0.01 | 0.02 | 0.07 | 0.01 | 0.05 | 0.03 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.08 | 0.02 | 0.27 | 0.05 | 0.09 | 0.01 | 0.04 | 0.01 | 0.05 | 0.01 | 0.05 | 0.07 | 0.00 | 0.01 | 0.00 | 0.00 | 0.03 | 0.10 | 0.01 | 0.00 | 0.01 | 0.01 | 0.11 | 0.00 | 0.11 | 0.01 |
| OR13C3 | ENSG00000204246 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.01 | 0.04 | 0.05 | 0.00 | 0.01 | 0.02 | 0.05 | 0.03 | 0.02 | 0.06 | 0.00 | 0.05 | 0.00 | 0.08 | 0.01 | 0.03 | 0.03 | 0.00 | 0.01 | 0.04 | 0.04 | 0.00 | 0.01 | 0.01 | 0.04 | 0.00 | 0.08 | 0.05 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.05 | 0.08 | 0.12 | 0.03 | 0.02 | 0.01 | 0.04 | 0.00 | 0.15 | 0.12 | 0.01 | 0.04 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 |
| COL5A2 | ENSG00000204262 | 0.03 | 0.02 | 0.10 | 0.00 | 0.00 | 0.01 | 0.02 | 0.04 | 0.08 | 0.06 | 0.00 | 0.00 | 0.00 | 0.02 | 0.05 | 0.01 | 0.14 | 0.04 | 0.14 | 0.04 | 0.12 | 0.02 | 0.07 | 0.05 | 0.01 | 0.00 | 0.04 | 0.03 | 0.03 | 0.01 | 0.05 | 0.02 | 0.00 | 0.01 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.07 | 0.02 | 0.40 | 0.05 | 0.11 | 0.02 | 0.06 | 0.01 | 0.00 | 0.03 | 0.04 | 0.10 | 0.06 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.01 | 0.00 | 0.01 | 0.03 | 0.00 | 0.02 | 0.02 |
| PSMB8 | ENSG00000204264 | 0.01 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.00 | 0.09 | 0.04 | 0.00 | 0.00 | 0.02 | 0.02 | 0.08 | 0.02 | 0.05 | 0.05 | 0.03 | 0.04 | 0.15 | 0.05 | 0.09 | 0.04 | 0.03 | 0.02 | 0.06 | 0.02 | 0.04 | 0.01 | 0.08 | 0.01 | 0.05 | 0.03 | 0.03 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.09 | 0.03 | 0.28 | 0.06 | 0.09 | 0.01 | 0.05 | 0.01 | 0.05 | 0.03 | 0.05 | 0.07 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.17 | 0.01 | 0.01 | 0.01 | 0.01 | 0.11 | 0.00 | 0.11 | 0.01 |
| SPIN3 | ENSG00000204271 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.04 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.01 | 0.04 | 0.03 | 0.07 | 0.01 | 0.11 | 0.03 | 0.03 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.12 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.07 | 0.00 | 0.25 | 0.03 | 0.04 | 0.03 | 0.08 | 0.01 | 0.29 | 0.03 | 0.18 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.06 | 0.00 | 0.06 | 0.01 | 0.02 | 0.00 | 0.03 | 0.00 | 0.02 | 0.00 |
| HLA-DRA | ENSG00000204287 | 0.01 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.00 | 0.09 | 0.04 | 0.00 | 0.00 | 0.02 | 0.02 | 0.08 | 0.02 | 0.05 | 0.05 | 0.03 | 0.04 | 0.15 | 0.05 | 0.09 | 0.04 | 0.03 | 0.02 | 0.06 | 0.02 | 0.04 | 0.01 | 0.08 | 0.01 | 0.05 | 0.03 | 0.03 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.09 | 0.03 | 0.28 | 0.06 | 0.09 | 0.01 | 0.05 | 0.01 | 0.05 | 0.03 | 0.05 | 0.07 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.17 | 0.01 | 0.01 | 0.01 | 0.01 | 0.11 | 0.00 | 0.11 | 0.01 |
| OR8B2 | ENSG00000204293 | 0.00 | 0.01 | 0.00 | 0.05 | 0.00 | 0.02 | 0.02 | 0.06 | 0.03 | 0.10 | 0.00 | 0.00 | 0.11 | 0.06 | 0.05 | 0.09 | 0.05 | 0.11 | 0.04 | 0.14 | 0.05 | 0.15 | 0.05 | 0.08 | 0.01 | 0.01 | 0.01 | 0.03 | 0.01 | 0.02 | 0.00 | 0.09 | 0.00 | 0.19 | 0.02 | 0.06 | 0.00 | 0.05 | 0.00 | 0.00 | 0.02 | 0.22 | 0.18 | 0.17 | 0.04 | 0.31 | 0.04 | 0.07 | 0.05 | 0.17 | 0.03 | 0.24 | 0.00 | 0.24 | 0.03 | 0.00 | 0.13 | 0.02 | 0.08 | 0.01 | 0.01 | 0.02 | 0.00 | 0.07 | 0.00 | 0.26 |
| CD300LD | ENSG00000204345 | 0.02 | 0.00 | 0.05 | 0.00 | 0.02 | 0.00 | 0.03 | 0.03 | 0.21 | 0.00 | 0.00 | 0.01 | 0.09 | 0.02 | 0.16 | 0.02 | 0.22 | 0.01 | 0.07 | 0.03 | 0.20 | 0.06 | 0.12 | 0.03 | 0.03 | 0.01 | 0.05 | 0.04 | 0.05 | 0.10 | 0.25 | 0.00 | 0.08 | 0.01 | 0.08 | 0.02 | 0.02 | 0.00 | 0.00 | 0.00 | 0.36 | 0.04 | 0.31 | 0.03 | 0.20 | 0.03 | 0.14 | 0.01 | 0.39 | 0.03 | 0.24 | 0.04 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.07 | 0.00 | 0.05 | 0.01 | 0.14 | 0.01 | 0.24 | 0.02 |
| NEU1 | ENSG00000204386 | 0.01 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.00 | 0.15 | 0.04 | 0.00 | 0.00 | 0.02 | 0.02 | 0.08 | 0.02 | 0.06 | 0.05 | 0.03 | 0.04 | 0.13 | 0.05 | 0.12 | 0.04 | 0.03 | 0.02 | 0.07 | 0.02 | 0.05 | 0.01 | 0.11 | 0.01 | 0.05 | 0.03 | 0.08 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.09 | 0.03 | 0.29 | 0.06 | 0.17 | 0.01 | 0.05 | 0.01 | 0.10 | 0.03 | 0.06 | 0.07 | 0.01 | 0.01 | 0.00 | 0.00 | 0.02 | 0.17 | 0.01 | 0.01 | 0.00 | 0.01 | 0.11 | 0.00 | 0.12 | 0.01 |
| HSPA1A | ENSG00000204389 | 0.01 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.00 | 0.15 | 0.04 | 0.00 | 0.00 | 0.02 | 0.02 | 0.08 | 0.02 | 0.06 | 0.05 | 0.03 | 0.04 | 0.13 | 0.05 | 0.12 | 0.04 | 0.03 | 0.02 | 0.07 | 0.02 | 0.05 | 0.01 | 0.11 | 0.01 | 0.05 | 0.03 | 0.08 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.09 | 0.03 | 0.29 | 0.06 | 0.17 | 0.01 | 0.05 | 0.01 | 0.10 | 0.03 | 0.06 | 0.07 | 0.01 | 0.01 | 0.00 | 0.00 | 0.02 | 0.17 | 0.01 | 0.01 | 0.00 | 0.01 | 0.11 | 0.00 | 0.12 | 0.01 |
| CASP12 | ENSG00000204403 | 0.00 | 0.01 | 0.00 | 0.06 | 0.01 | 0.03 | 0.01 | 0.06 | 0.08 | 0.10 | 0.00 | 0.00 | 0.02 | 0.08 | 0.06 | 0.07 | 0.07 | 0.07 | 0.09 | 0.14 | 0.13 | 0.07 | 0.03 | 0.06 | 0.02 | 0.03 | 0.02 | 0.03 | 0.01 | 0.02 | 0.02 | 0.06 | 0.00 | 0.14 | 0.00 | 0.05 | 0.00 | 0.05 | 0.00 | 0.00 | 0.04 | 0.20 | 0.25 | 0.15 | 0.11 | 0.22 | 0.02 | 0.06 | 0.14 | 0.27 | 0.10 | 0.18 | 0.01 | 0.10 | 0.02 | 0.00 | 0.04 | 0.01 | 0.01 | 0.01 | 0.00 | 0.01 | 0.00 | 0.01 | 0.07 | 0.19 |
| CSHL1 | ENSG00000204414 | 0.02 | 0.00 | 0.05 | 0.00 | 0.00 | 0.00 | 0.03 | 0.02 | 0.25 | 0.01 | 0.02 | 0.00 | 0.12 | 0.00 | 0.15 | 0.01 | 0.20 | 0.01 | 0.07 | 0.02 | 0.22 | 0.02 | 0.11 | 0.02 | 0.07 | 0.01 | 0.07 | 0.02 | 0.08 | 0.10 | 0.20 | 0.00 | 0.12 | 0.01 | 0.16 | 0.03 | 0.02 | 0.00 | 0.00 | 0.00 | 0.57 | 0.01 | 0.24 | 0.03 | 0.17 | 0.02 | 0.10 | 0.03 | 0.27 | 0.02 | 0.17 | 0.03 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.02 | 0.06 | 0.00 | 0.03 | 0.01 | 0.16 | 0.00 | 0.24 | 0.01 |
| C6orf25 | ENSG00000204420 | 0.01 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.00 | 0.15 | 0.04 | 0.00 | 0.00 | 0.02 | 0.02 | 0.08 | 0.02 | 0.06 | 0.05 | 0.03 | 0.04 | 0.13 | 0.05 | 0.12 | 0.04 | 0.03 | 0.02 | 0.07 | 0.02 | 0.05 | 0.01 | 0.11 | 0.01 | 0.05 | 0.03 | 0.08 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.09 | 0.03 | 0.29 | 0.06 | 0.17 | 0.01 | 0.05 | 0.01 | 0.10 | 0.03 | 0.06 | 0.07 | 0.01 | 0.01 | 0.00 | 0.00 | 0.02 | 0.17 | 0.01 | 0.01 | 0.00 | 0.01 | 0.11 | 0.00 | 0.12 | 0.01 |
| CSNK2B | ENSG00000204435 | 0.01 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.00 | 0.15 | 0.04 | 0.00 | 0.00 | 0.02 | 0.02 | 0.08 | 0.02 | 0.06 | 0.05 | 0.03 | 0.04 | 0.13 | 0.05 | 0.12 | 0.04 | 0.03 | 0.02 | 0.07 | 0.02 | 0.05 | 0.01 | 0.11 | 0.01 | 0.05 | 0.03 | 0.08 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.09 | 0.03 | 0.29 | 0.06 | 0.17 | 0.01 | 0.05 | 0.01 | 0.10 | 0.03 | 0.06 | 0.07 | 0.01 | 0.01 | 0.00 | 0.00 | 0.02 | 0.17 | 0.01 | 0.01 | 0.00 | 0.01 | 0.11 | 0.00 | 0.12 | 0.01 |
| APOM | ENSG00000204444 | 0.01 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.00 | 0.15 | 0.04 | 0.00 | 0.00 | 0.02 | 0.02 | 0.08 | 0.02 | 0.06 | 0.05 | 0.03 | 0.04 | 0.13 | 0.05 | 0.12 | 0.04 | 0.03 | 0.02 | 0.07 | 0.02 | 0.05 | 0.01 | 0.11 | 0.01 | 0.05 | 0.03 | 0.08 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.09 | 0.03 | 0.29 | 0.06 | 0.17 | 0.01 | 0.05 | 0.01 | 0.10 | 0.03 | 0.06 | 0.07 | 0.01 | 0.01 | 0.00 | 0.00 | 0.02 | 0.17 | 0.01 | 0.01 | 0.00 | 0.01 | 0.11 | 0.00 | 0.12 | 0.01 |
| NCR3 | ENSG00000204475 | 0.01 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.00 | 0.15 | 0.04 | 0.00 | 0.00 | 0.02 | 0.02 | 0.08 | 0.02 | 0.06 | 0.05 | 0.03 | 0.04 | 0.13 | 0.05 | 0.12 | 0.04 | 0.03 | 0.02 | 0.07 | 0.02 | 0.05 | 0.01 | 0.11 | 0.01 | 0.05 | 0.03 | 0.08 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.09 | 0.03 | 0.29 | 0.06 | 0.17 | 0.01 | 0.05 | 0.01 | 0.10 | 0.03 | 0.06 | 0.07 | 0.01 | 0.01 | 0.00 | 0.00 | 0.02 | 0.17 | 0.01 | 0.01 | 0.00 | 0.01 | 0.11 | 0.00 | 0.12 | 0.01 |
| C6orf15 | ENSG00000204542 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.19 | 0.02 | 0.00 | 0.00 | 0.02 | 0.02 | 0.08 | 0.01 | 0.07 | 0.05 | 0.03 | 0.04 | 0.17 | 0.05 | 0.12 | 0.04 | 0.04 | 0.01 | 0.07 | 0.01 | 0.06 | 0.01 | 0.11 | 0.01 | 0.08 | 0.03 | 0.11 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.09 | 0.03 | 0.30 | 0.06 | 0.17 | 0.01 | 0.05 | 0.01 | 0.16 | 0.03 | 0.06 | 0.05 | 0.01 | 0.01 | 0.00 | 0.00 | 0.05 | 0.14 | 0.01 | 0.00 | 0.00 | 0.01 | 0.11 | 0.00 | 0.13 | 0.01 |
| TRIM39 | ENSG00000204599 | 0.01 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.16 | 0.02 | 0.00 | 0.00 | 0.02 | 0.02 | 0.07 | 0.02 | 0.06 | 0.05 | 0.03 | 0.04 | 0.15 | 0.07 | 0.12 | 0.05 | 0.03 | 0.01 | 0.06 | 0.01 | 0.03 | 0.01 | 0.12 | 0.00 | 0.06 | 0.03 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.09 | 0.02 | 0.29 | 0.06 | 0.13 | 0.03 | 0.04 | 0.01 | 0.17 | 0.02 | 0.03 | 0.06 | 0.01 | 0.01 | 0.00 | 0.00 | 0.05 | 0.04 | 0.01 | 0.01 | 0.00 | 0.01 | 0.13 | 0.00 | 0.13 | 0.01 |
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