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 |
| CPN2 | ENSG00000178772 | 0.05 | 0.00 | 0.03 | 0.01 | 0.00 | 0.01 | 0.02 | 0.05 | 0.17 | 0.02 | 0.00 | 0.00 | 0.00 | 0.04 | 0.14 | 0.06 | 1.35 | 0.01 | 0.57 | 0.00 | 0.76 | 0.02 | 0.25 | 0.02 | 0.05 | 0.01 | 0.06 | 0.02 | 0.03 | 0.01 | 0.12 | 0.03 | 0.18 | 0.03 | 0.10 | 0.00 | 0.00 | 0.09 | 0.00 | 0.00 | 0.21 | 0.02 | 0.99 | 0.08 | 0.65 | 0.00 | 0.37 | 0.00 | 0.80 | 0.15 | 0.12 | 0.10 | 0.17 | 0.02 | 0.00 | 0.00 | 0.07 | 0.01 | 0.02 | 0.05 | 0.07 | 0.09 | 0.00 | 0.00 | 0.03 | 0.03 |
| CD300LB | ENSG00000178789 | 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 |
| MPI | ENSG00000178802 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.02 | 0.01 | 0.03 | 0.04 | 0.02 | 0.00 | 0.00 | 0.09 | 0.00 | 0.03 | 0.02 | 0.07 | 0.02 | 0.02 | 0.03 | 0.08 | 0.03 | 0.05 | 0.04 | 0.02 | 0.02 | 0.03 | 0.03 | 0.03 | 0.02 | 0.05 | 0.03 | 0.00 | 0.01 | 0.07 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.08 | 0.04 | 0.16 | 0.15 | 0.12 | 0.01 | 0.04 | 0.04 | 0.20 | 0.07 | 0.05 | 0.08 | 0.00 | 0.00 | 0.00 | 0.01 | 0.06 | 0.00 | 0.01 | 0.01 | 0.01 | 0.03 | 0.00 | 0.00 | 0.13 | 0.01 |
| LGALS7B | ENSG00000178934 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.02 | 0.02 | 0.02 | 0.32 | 0.02 | 0.00 | 0.00 | 0.08 | 0.02 | 0.20 | 0.03 | 0.54 | 0.03 | 0.07 | 0.01 | 0.09 | 0.04 | 0.11 | 0.02 | 0.05 | 0.01 | 0.03 | 0.01 | 0.20 | 0.00 | 0.06 | 0.01 | 0.12 | 0.01 | 0.05 | 0.03 | 0.01 | 0.02 | 0.00 | 0.00 | 0.12 | 0.03 | 0.72 | 0.12 | 0.28 | 0.03 | 0.17 | 0.03 | 1.10 | 0.11 | 0.23 | 0.09 | 0.00 | 0.03 | 0.01 | 0.00 | 0.03 | 0.00 | 0.02 | 0.04 | 0.04 | 0.04 | 0.00 | 0.00 | 0.04 | 0.01 |
| TAS1R2 | ENSG00000179002 | 0.00 | 0.06 | 0.00 | 0.08 | 0.00 | 0.00 | 0.01 | 0.05 | 0.08 | 0.08 | 0.00 | 0.01 | 0.04 | 0.25 | 0.04 | 0.06 | 0.04 | 0.11 | 0.03 | 0.08 | 0.07 | 0.09 | 0.06 | 0.10 | 0.00 | 0.16 | 0.00 | 0.22 | 0.02 | 0.07 | 0.03 | 0.21 | 0.00 | 1.10 | 0.01 | 0.07 | 0.01 | 0.10 | 0.00 | 0.00 | 0.01 | 0.20 | 0.10 | 0.44 | 0.04 | 0.08 | 0.06 | 0.13 | 0.07 | 0.19 | 0.19 | 0.11 | 0.05 | 0.07 | 0.02 | 0.01 | 0.00 | 0.03 | 0.00 | 0.02 | 0.06 | 0.07 | 0.00 | 0.12 | 0.07 | 0.10 |
| OR13D1 | ENSG00000179055 | 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 | 0.02 | 0.02 | 0.06 | 0.00 | 0.05 | 0.00 | 0.09 | 0.01 | 0.03 | 0.03 | 0.00 | 0.01 | 0.04 | 0.04 | 0.00 | 0.01 | 0.03 | 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 | 0.02 | 0.04 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 |
| TAAR3 | ENSG00000179073 | 0.00 | 0.05 | 0.00 | 0.00 | 0.00 | 0.05 | 0.01 | 0.01 | 0.07 | 0.05 | 0.00 | 0.01 | 0.00 | 0.14 | 0.03 | 0.04 | 0.05 | 0.03 | 0.05 | 0.01 | 0.10 | 0.02 | 0.08 | 0.02 | 0.02 | 0.01 | 0.04 | 0.03 | 0.00 | 0.02 | 0.01 | 0.08 | 0.00 | 0.10 | 0.04 | 0.04 | 0.00 | 0.01 | 0.00 | 0.00 | 0.10 | 0.05 | 0.06 | 0.28 | 0.01 | 0.02 | 0.05 | 0.03 | 0.08 | 0.03 | 0.30 | 0.05 | 0.01 | 0.04 | 0.00 | 0.00 | 0.00 | 0.15 | 0.00 | 0.05 | 0.00 | 0.10 | 0.00 | 0.09 | 0.01 | 0.12 |
| HTR1F | ENSG00000179097 | 0.00 | 0.02 | 0.02 | 0.00 | 0.00 | 0.02 | 0.02 | 0.04 | 0.14 | 0.10 | 0.00 | 0.01 | 0.00 | 0.04 | 0.05 | 0.05 | 0.11 | 0.17 | 0.02 | 0.08 | 0.05 | 0.19 | 0.06 | 0.04 | 0.01 | 0.02 | 0.02 | 0.02 | 0.01 | 0.01 | 0.01 | 0.04 | 0.00 | 0.08 | 0.07 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.04 | 0.07 | 0.10 | 0.07 | 0.03 | 0.14 | 0.03 | 0.05 | 0.05 | 0.24 | 0.36 | 0.08 | 0.05 | 0.00 | 0.02 | 0.01 | 0.02 | 0.00 | 0.00 | 0.02 | 0.01 | 0.03 | 0.00 | 0.00 | 0.05 | 0.02 |
| CYP11B2 | ENSG00000179142 | 0.02 | 0.00 | 0.02 | 0.00 | 0.06 | 0.00 | 0.04 | 0.02 | 0.20 | 0.02 | 0.02 | 0.00 | 0.10 | 0.04 | 0.26 | 0.01 | 0.36 | 0.02 | 0.29 | 0.00 | 0.41 | 0.02 | 0.21 | 0.02 | 0.15 | 0.03 | 0.24 | 0.03 | 0.15 | 0.02 | 0.34 | 0.02 | 0.25 | 0.01 | 0.08 | 0.00 | 0.01 | 0.03 | 0.00 | 0.01 | 0.43 | 0.05 | 1.47 | 0.05 | 0.21 | 0.01 | 0.10 | 0.02 | 0.14 | 0.03 | 0.20 | 0.06 | 0.05 | 0.03 | 0.02 | 0.00 | 0.26 | 0.01 | 0.17 | 0.04 | 0.03 | 0.03 | 0.50 | 0.00 | 0.24 | 0.02 |
| ALOXE3 | ENSG00000179148 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.17 | 0.03 | 0.02 | 0.00 | 0.01 | 0.00 | 0.03 | 0.01 | 0.05 | 0.01 | 0.02 | 0.01 | 0.03 | 0.03 | 0.04 | 0.01 | 0.03 | 0.00 | 0.02 | 0.00 | 0.02 | 0.01 | 0.02 | 0.00 | 0.16 | 0.00 | 0.03 | 0.01 | 0.05 | 0.01 | 0.03 | 0.00 | 0.00 | 0.01 | 0.06 | 0.08 | 0.06 | 0.00 | 0.04 | 0.04 | 0.04 | 0.06 | 0.15 | 0.20 | 0.27 | 0.00 | 0.02 | 0.02 | 0.01 | 0.00 | 0.10 | 0.01 | 0.00 | 0.00 | 0.06 | 0.00 | 0.00 | 0.00 | 0.04 |
| DAND5 | ENSG00000179284 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.05 | 0.04 | 0.01 | 0.00 | 0.09 | 0.02 | 0.01 | 0.05 | 0.09 | 0.05 | 0.08 | 0.02 | 0.12 | 0.05 | 0.05 | 0.03 | 0.00 | 0.01 | 0.01 | 0.02 | 0.01 | 0.02 | 0.04 | 0.10 | 0.00 | 0.01 | 0.17 | 0.03 | 0.00 | 0.00 | 0.00 | 0.01 | 0.08 | 0.04 | 0.83 | 0.10 | 0.11 | 0.04 | 0.24 | 0.03 | 0.25 | 0.14 | 0.21 | 0.02 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.03 | 0.01 | 0.01 | 0.03 | 0.01 | 0.02 | 0.00 | 0.02 | 0.02 |
| CLK3 | ENSG00000179335 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.02 | 0.01 | 0.03 | 0.04 | 0.02 | 0.00 | 0.00 | 0.09 | 0.00 | 0.05 | 0.02 | 0.06 | 0.02 | 0.02 | 0.03 | 0.08 | 0.03 | 0.05 | 0.03 | 0.02 | 0.02 | 0.03 | 0.03 | 0.03 | 0.02 | 0.04 | 0.04 | 0.00 | 0.01 | 0.05 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.08 | 0.04 | 0.15 | 0.15 | 0.12 | 0.01 | 0.04 | 0.04 | 0.14 | 0.03 | 0.05 | 0.10 | 0.00 | 0.02 | 0.00 | 0.01 | 0.06 | 0.00 | 0.01 | 0.01 | 0.02 | 0.03 | 0.00 | 0.00 | 0.12 | 0.01 |
| VWA1 | ENSG00000179403 | 0.00 | 0.05 | 0.01 | 0.10 | 0.00 | 0.00 | 0.02 | 0.03 | 0.10 | 0.08 | 0.00 | 0.02 | 0.04 | 0.27 | 0.09 | 0.06 | 0.08 | 0.11 | 0.06 | 0.09 | 0.13 | 0.08 | 0.09 | 0.09 | 0.02 | 0.11 | 0.00 | 0.17 | 0.05 | 0.05 | 0.02 | 0.31 | 0.00 | 1.01 | 0.05 | 0.17 | 0.01 | 0.12 | 0.00 | 0.00 | 0.04 | 0.19 | 0.23 | 0.38 | 0.06 | 0.11 | 0.05 | 0.12 | 0.08 | 0.27 | 0.18 | 0.28 | 0.10 | 0.12 | 0.02 | 0.00 | 0.00 | 0.19 | 0.00 | 0.03 | 0.03 | 0.15 | 0.00 | 0.14 | 0.07 | 0.13 |
| OR6W1P | ENSG00000179420 | 0.02 | 0.01 | 0.05 | 0.00 | 0.05 | 0.02 | 0.02 | 0.03 | 0.05 | 0.03 | 0.00 | 0.01 | 0.04 | 0.03 | 0.08 | 0.02 | 0.08 | 0.06 | 0.02 | 0.15 | 0.04 | 0.20 | 0.03 | 0.09 | 0.02 | 0.01 | 0.01 | 0.03 | 0.03 | 0.04 | 0.04 | 0.05 | 0.00 | 0.11 | 0.06 | 0.06 | 0.00 | 0.02 | 0.00 | 0.00 | 0.09 | 0.04 | 0.53 | 0.04 | 0.03 | 0.09 | 0.04 | 0.05 | 0.05 | 0.14 | 0.12 | 0.11 | 0.02 | 0.04 | 0.00 | 0.05 | 0.02 | 0.09 | 0.11 | 0.01 | 0.04 | 0.02 | 0.00 | 0.03 | 0.22 | 0.02 |
| FJX1 | ENSG00000179431 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.05 | 0.12 | 0.03 | 0.00 | 0.00 | 0.03 | 0.02 | 0.07 | 0.01 | 0.15 | 0.02 | 0.15 | 0.00 | 0.25 | 0.02 | 0.21 | 0.00 | 0.01 | 0.01 | 0.01 | 0.00 | 0.02 | 0.01 | 0.01 | 0.00 | 0.00 | 0.02 | 0.04 | 0.01 | 0.02 | 0.05 | 0.00 | 0.00 | 0.15 | 0.01 | 0.17 | 0.06 | 0.14 | 0.01 | 0.06 | 0.02 | 0.04 | 0.02 | 0.15 | 0.09 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.03 | 0.01 | 0.00 | 0.02 | 0.05 | 0.02 |
| KLHL28 | ENSG00000179454 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.02 | 0.06 | 0.00 | 0.00 | 0.00 | 0.01 | 0.15 | 0.03 | 0.05 | 0.08 | 0.05 | 0.03 | 0.10 | 0.03 | 0.05 | 0.05 | 0.01 | 0.03 | 0.01 | 0.02 | 0.01 | 0.01 | 0.04 | 0.03 | 0.10 | 0.02 | 0.08 | 0.10 | 0.01 | 0.01 | 0.00 | 0.00 | 0.08 | 0.03 | 0.13 | 0.10 | 0.01 | 0.02 | 0.02 | 0.03 | 0.00 | 0.15 | 0.10 | 0.05 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.01 | 0.06 | 0.00 | 0.00 | 0.02 | 0.01 |
| OR9A2 | ENSG00000179468 | 0.02 | 0.01 | 0.05 | 0.00 | 0.05 | 0.02 | 0.02 | 0.03 | 0.05 | 0.03 | 0.00 | 0.01 | 0.04 | 0.03 | 0.07 | 0.02 | 0.08 | 0.06 | 0.02 | 0.15 | 0.04 | 0.20 | 0.03 | 0.09 | 0.02 | 0.01 | 0.01 | 0.03 | 0.03 | 0.04 | 0.04 | 0.05 | 0.00 | 0.11 | 0.06 | 0.06 | 0.00 | 0.02 | 0.00 | 0.00 | 0.09 | 0.04 | 0.53 | 0.04 | 0.03 | 0.09 | 0.04 | 0.05 | 0.05 | 0.14 | 0.12 | 0.11 | 0.02 | 0.04 | 0.00 | 0.05 | 0.02 | 0.09 | 0.11 | 0.01 | 0.04 | 0.02 | 0.00 | 0.03 | 0.22 | 0.02 |
| ALOX12B | ENSG00000179477 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.19 | 0.03 | 0.03 | 0.00 | 0.01 | 0.00 | 0.03 | 0.01 | 0.05 | 0.01 | 0.02 | 0.01 | 0.03 | 0.03 | 0.04 | 0.01 | 0.02 | 0.00 | 0.03 | 0.00 | 0.02 | 0.01 | 0.02 | 0.00 | 0.16 | 0.00 | 0.03 | 0.01 | 0.05 | 0.01 | 0.03 | 0.00 | 0.00 | 0.01 | 0.06 | 0.08 | 0.06 | 0.00 | 0.04 | 0.03 | 0.04 | 0.06 | 0.15 | 0.20 | 0.28 | 0.00 | 0.02 | 0.02 | 0.01 | 0.00 | 0.10 | 0.01 | 0.00 | 0.00 | 0.06 | 0.00 | 0.00 | 0.00 | 0.04 |
| SLC17A8 | ENSG00000179520 | 0.01 | 0.01 | 0.02 | 0.00 | 0.06 | 0.02 | 0.05 | 0.02 | 0.06 | 0.03 | 0.00 | 0.00 | 0.01 | 0.05 | 0.02 | 0.05 | 0.01 | 0.04 | 0.02 | 0.02 | 0.04 | 0.05 | 0.04 | 0.04 | 0.01 | 0.01 | 0.01 | 0.03 | 0.00 | 0.06 | 0.08 | 0.03 | 0.00 | 0.22 | 0.00 | 0.02 | 0.00 | 0.03 | 0.00 | 0.00 | 0.04 | 0.07 | 0.08 | 0.22 | 0.01 | 0.01 | 0.02 | 0.03 | 0.02 | 0.11 | 0.34 | 0.05 | 0.00 | 0.00 | 0.00 | 0.00 | 0.08 | 0.02 | 0.01 | 0.02 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.08 |
| HTR1D | ENSG00000179546 | 0.00 | 0.06 | 0.00 | 0.08 | 0.00 | 0.00 | 0.00 | 0.04 | 0.07 | 0.09 | 0.00 | 0.03 | 0.04 | 0.23 | 0.04 | 0.06 | 0.05 | 0.11 | 0.03 | 0.07 | 0.03 | 0.10 | 0.06 | 0.11 | 0.00 | 0.16 | 0.00 | 0.21 | 0.01 | 0.08 | 0.01 | 0.22 | 0.00 | 1.06 | 0.05 | 0.04 | 0.01 | 0.10 | 0.00 | 0.00 | 0.01 | 0.19 | 0.12 | 0.44 | 0.04 | 0.08 | 0.04 | 0.12 | 0.09 | 0.19 | 0.16 | 0.11 | 0.05 | 0.06 | 0.02 | 0.00 | 0.00 | 0.15 | 0.04 | 0.03 | 0.02 | 0.10 | 0.00 | 0.12 | 0.07 | 0.08 |
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