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 |
| CD27 | ENSG00000139193 | 0.01 | 0.00 | 0.00 | 0.01 | 0.02 | 0.00 | 0.01 | 0.07 | 0.09 | 0.02 | 0.01 | 0.00 | 0.00 | 0.08 | 0.07 | 0.07 | 0.17 | 0.01 | 0.11 | 0.01 | 0.08 | 0.05 | 0.06 | 0.05 | 0.06 | 0.02 | 0.05 | 0.02 | 0.05 | 0.05 | 0.03 | 0.04 | 0.14 | 0.05 | 0.05 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.13 | 0.04 | 0.37 | 0.08 | 0.05 | 0.02 | 0.09 | 0.02 | 0.12 | 0.03 | 0.10 | 0.12 | 0.60 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.16 | 0.01 | 0.06 | 0.02 | 0.00 | 0.01 | 0.05 | 0.04 |
| RBP5 | ENSG00000139194 | 0.01 | 0.00 | 0.00 | 0.01 | 0.02 | 0.00 | 0.01 | 0.07 | 0.09 | 0.02 | 0.01 | 0.00 | 0.00 | 0.08 | 0.06 | 0.07 | 0.16 | 0.01 | 0.11 | 0.02 | 0.07 | 0.02 | 0.05 | 0.06 | 0.05 | 0.02 | 0.04 | 0.03 | 0.05 | 0.06 | 0.04 | 0.05 | 0.18 | 0.05 | 0.05 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.12 | 0.04 | 0.32 | 0.08 | 0.04 | 0.02 | 0.07 | 0.02 | 0.11 | 0.03 | 0.09 | 0.11 | 0.60 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.14 | 0.01 | 0.06 | 0.02 | 0.00 | 0.01 | 0.04 | 0.04 |
| INHBE | ENSG00000139269 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.06 | 0.03 | 0.00 | 0.00 | 0.02 | 0.02 | 0.17 | 0.01 | 0.03 | 0.01 | 0.04 | 0.02 | 0.11 | 0.04 | 0.11 | 0.01 | 0.02 | 0.00 | 0.02 | 0.01 | 0.04 | 0.02 | 0.07 | 0.01 | 0.06 | 0.01 | 0.40 | 0.02 | 0.06 | 0.00 | 0.00 | 0.00 | 0.06 | 0.04 | 0.14 | 0.04 | 0.03 | 0.00 | 0.03 | 0.01 | 0.10 | 0.06 | 0.32 | 0.07 | 0.00 | 0.00 | 0.00 | 0.00 | 0.12 | 0.00 | 0.16 | 0.02 | 0.48 | 0.04 | 0.00 | 0.00 | 0.14 | 0.02 |
| PTPRQ | ENSG00000139304 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.00 | 0.03 | 0.02 | 0.07 | 0.05 | 0.00 | 0.00 | 0.02 | 0.05 | 0.03 | 0.04 | 0.03 | 0.03 | 0.01 | 0.03 | 0.04 | 0.06 | 0.01 | 0.04 | 0.00 | 0.03 | 0.02 | 0.05 | 0.00 | 0.06 | 0.04 | 0.02 | 0.00 | 0.08 | 0.09 | 0.02 | 0.00 | 0.02 | 0.00 | 0.00 | 0.08 | 0.05 | 0.09 | 0.18 | 0.01 | 0.03 | 0.02 | 0.03 | 0.05 | 0.11 | 0.57 | 0.04 | 0.04 | 0.00 | 0.00 | 0.01 | 0.04 | 0.02 | 0.00 | 0.02 | 0.04 | 0.05 | 0.02 | 0.00 | 0.04 | 0.06 |
| DUSP6 | ENSG00000139318 | 0.01 | 0.01 | 0.00 | 0.00 | 0.06 | 0.00 | 0.04 | 0.01 | 0.08 | 0.04 | 0.00 | 0.00 | 0.01 | 0.05 | 0.02 | 0.05 | 0.04 | 0.03 | 0.01 | 0.03 | 0.04 | 0.07 | 0.02 | 0.03 | 0.00 | 0.02 | 0.03 | 0.05 | 0.00 | 0.07 | 0.03 | 0.02 | 0.00 | 0.13 | 0.06 | 0.02 | 0.00 | 0.02 | 0.00 | 0.00 | 0.10 | 0.05 | 0.08 | 0.22 | 0.02 | 0.02 | 0.02 | 0.04 | 0.03 | 0.16 | 0.39 | 0.05 | 0.01 | 0.01 | 0.00 | 0.01 | 0.08 | 0.05 | 0.00 | 0.02 | 0.00 | 0.05 | 0.00 | 0.00 | 0.00 | 0.09 |
| LUM | ENSG00000139329 | 0.01 | 0.01 | 0.00 | 0.00 | 0.06 | 0.02 | 0.04 | 0.00 | 0.08 | 0.04 | 0.00 | 0.00 | 0.01 | 0.03 | 0.02 | 0.05 | 0.04 | 0.03 | 0.01 | 0.03 | 0.03 | 0.06 | 0.03 | 0.03 | 0.00 | 0.03 | 0.03 | 0.06 | 0.00 | 0.08 | 0.03 | 0.02 | 0.00 | 0.17 | 0.02 | 0.02 | 0.01 | 0.02 | 0.00 | 0.00 | 0.10 | 0.05 | 0.06 | 0.23 | 0.02 | 0.02 | 0.02 | 0.03 | 0.00 | 0.16 | 0.26 | 0.04 | 0.00 | 0.01 | 0.00 | 0.02 | 0.08 | 0.05 | 0.00 | 0.02 | 0.00 | 0.04 | 0.00 | 0.00 | 0.01 | 0.08 |
| KERA | ENSG00000139330 | 0.01 | 0.01 | 0.00 | 0.00 | 0.06 | 0.02 | 0.04 | 0.00 | 0.08 | 0.04 | 0.00 | 0.00 | 0.01 | 0.03 | 0.02 | 0.05 | 0.04 | 0.04 | 0.01 | 0.03 | 0.03 | 0.07 | 0.04 | 0.03 | 0.00 | 0.03 | 0.03 | 0.09 | 0.00 | 0.08 | 0.03 | 0.02 | 0.00 | 0.17 | 0.02 | 0.02 | 0.00 | 0.07 | 0.00 | 0.00 | 0.10 | 0.05 | 0.06 | 0.23 | 0.02 | 0.02 | 0.02 | 0.04 | 0.00 | 0.16 | 0.36 | 0.04 | 0.00 | 0.01 | 0.00 | 0.02 | 0.08 | 0.05 | 0.00 | 0.02 | 0.00 | 0.04 | 0.00 | 0.00 | 0.01 | 0.08 |
| SLC46A3 | ENSG00000139508 | 0.01 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.05 | 0.13 | 0.05 | 0.00 | 0.02 | 0.00 | 0.18 | 0.03 | 0.08 | 0.03 | 0.12 | 0.02 | 0.14 | 0.10 | 0.06 | 0.10 | 0.04 | 0.20 | 0.00 | 0.52 | 0.02 | 0.01 | 0.01 | 0.02 | 0.14 | 0.00 | 0.15 | 0.00 | 0.09 | 0.00 | 0.00 | 0.00 | 0.01 | 0.11 | 0.06 | 0.05 | 0.16 | 0.03 | 0.14 | 0.01 | 0.05 | 0.01 | 0.14 | 0.10 | 0.23 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.09 | 0.01 | 0.05 | 0.01 | 0.06 | 0.00 | 0.00 | 0.06 | 0.03 |
| RDH16 | ENSG00000139547 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.04 | 0.03 | 0.00 | 0.00 | 0.02 | 0.02 | 0.11 | 0.01 | 0.03 | 0.01 | 0.03 | 0.02 | 0.08 | 0.04 | 0.10 | 0.02 | 0.02 | 0.00 | 0.02 | 0.01 | 0.03 | 0.01 | 0.08 | 0.01 | 0.06 | 0.01 | 0.19 | 0.03 | 0.06 | 0.00 | 0.00 | 0.00 | 0.04 | 0.04 | 0.15 | 0.04 | 0.04 | 0.00 | 0.05 | 0.01 | 0.20 | 0.06 | 0.19 | 0.07 | 0.02 | 0.00 | 0.00 | 0.00 | 0.12 | 0.00 | 0.02 | 0.02 | 0.06 | 0.04 | 0.00 | 0.00 | 0.07 | 0.02 |
| DHH | ENSG00000139549 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.04 | 0.00 | 0.00 | 0.00 | 0.04 | 0.06 | 0.01 | 0.02 | 0.02 | 0.01 | 0.05 | 0.06 | 0.05 | 0.04 | 0.04 | 0.02 | 0.00 | 0.02 | 0.01 | 0.00 | 0.05 | 0.01 | 0.01 | 0.09 | 0.01 | 0.17 | 0.00 | 0.00 | 0.03 | 0.00 | 0.00 | 0.04 | 0.05 | 0.09 | 0.06 | 0.02 | 0.01 | 0.03 | 0.01 | 0.09 | 0.11 | 0.03 | 0.09 | 0.02 | 0.00 | 0.00 | 0.01 | 0.10 | 0.06 | 0.01 | 0.04 | 0.02 | 0.05 | 0.00 | 0.00 | 0.05 | 0.04 |
| GPR84 | ENSG00000139572 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.01 | 0.00 | 0.09 | 0.02 | 0.00 | 0.00 | 0.02 | 0.02 | 0.07 | 0.01 | 0.04 | 0.02 | 0.02 | 0.02 | 0.06 | 0.03 | 0.07 | 0.02 | 0.02 | 0.00 | 0.02 | 0.01 | 0.00 | 0.02 | 0.02 | 0.01 | 0.17 | 0.01 | 0.15 | 0.00 | 0.05 | 0.00 | 0.00 | 0.00 | 0.04 | 0.05 | 0.20 | 0.05 | 0.04 | 0.00 | 0.08 | 0.01 | 0.14 | 0.09 | 0.24 | 0.08 | 0.01 | 0.00 | 0.00 | 0.00 | 0.09 | 0.00 | 0.01 | 0.04 | 0.03 | 0.05 | 0.08 | 0.00 | 0.03 | 0.05 |
| NPFF | ENSG00000139574 | 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 | 0.05 | 0.05 | 0.06 | 0.03 | 0.02 | 0.00 | 0.03 | 0.02 | 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 | 0.05 | 0.03 | 0.00 | 0.07 | 0.01 | 0.39 | 0.09 | 0.07 | 0.09 | 0.00 | 0.00 | 0.00 | 0.00 | 0.12 | 0.00 | 0.00 | 0.04 | 0.02 | 0.05 | 0.00 | 0.00 | 0.03 | 0.06 |
| CELA1 | ENSG00000139610 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.10 | 0.03 | 0.00 | 0.00 | 0.00 | 0.04 | 0.06 | 0.02 | 0.02 | 0.02 | 0.01 | 0.03 | 0.09 | 0.04 | 0.06 | 0.04 | 0.03 | 0.00 | 0.03 | 0.01 | 0.01 | 0.04 | 0.02 | 0.01 | 0.09 | 0.01 | 0.32 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.04 | 0.06 | 0.10 | 0.05 | 0.03 | 0.00 | 0.05 | 0.01 | 0.24 | 0.04 | 0.06 | 0.09 | 0.01 | 0.00 | 0.00 | 0.00 | 0.12 | 0.00 | 0.01 | 0.03 | 0.04 | 0.05 | 0.00 | 0.00 | 0.04 | 0.06 |
| SSTR1 | ENSG00000139874 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.02 | 0.06 | 0.00 | 0.00 | 0.00 | 0.03 | 0.57 | 0.01 | 0.14 | 0.07 | 0.05 | 0.03 | 0.21 | 0.03 | 0.10 | 0.01 | 0.03 | 0.02 | 0.02 | 0.03 | 0.01 | 0.01 | 0.04 | 0.04 | 0.05 | 0.07 | 0.09 | 0.02 | 0.01 | 0.01 | 0.00 | 0.00 | 0.15 | 0.02 | 0.12 | 0.11 | 0.08 | 0.01 | 0.04 | 0.02 | 0.01 | 0.03 | 0.18 | 0.04 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.08 | 0.00 | 0.00 | 0.01 | 0.01 |
| CBLN3 | ENSG00000139899 | 0.00 | 0.00 | 0.03 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.08 | 0.07 | 0.00 | 0.00 | 0.00 | 0.02 | 0.15 | 0.02 | 0.09 | 0.07 | 0.05 | 0.07 | 0.11 | 0.04 | 0.05 | 0.04 | 0.02 | 0.02 | 0.01 | 0.06 | 0.01 | 0.03 | 0.09 | 0.01 | 0.00 | 0.02 | 0.26 | 0.03 | 0.00 | 0.01 | 0.00 | 0.00 | 0.10 | 0.04 | 0.19 | 0.12 | 0.03 | 0.02 | 0.05 | 0.03 | 0.11 | 0.07 | 0.21 | 0.03 | 0.01 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.03 | 0.03 | 0.01 | 0.09 | 0.00 | 0.00 | 0.03 | 0.03 |
| TSSK4 | ENSG00000139908 | 0.00 | 0.00 | 0.03 | 0.01 | 0.00 | 0.00 | 0.01 | 0.01 | 0.09 | 0.06 | 0.01 | 0.00 | 0.00 | 0.02 | 0.16 | 0.03 | 0.12 | 0.07 | 0.05 | 0.07 | 0.11 | 0.06 | 0.05 | 0.04 | 0.02 | 0.02 | 0.01 | 0.06 | 0.00 | 0.03 | 0.08 | 0.01 | 0.00 | 0.02 | 0.28 | 0.03 | 0.00 | 0.02 | 0.00 | 0.00 | 0.10 | 0.03 | 0.17 | 0.13 | 0.03 | 0.03 | 0.06 | 0.03 | 0.23 | 0.07 | 0.21 | 0.03 | 0.01 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.03 | 0.03 | 0.00 | 0.09 | 0.00 | 0.00 | 0.03 | 0.03 |
| TMX1 | ENSG00000139921 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.02 | 0.03 | 0.00 | 0.01 | 0.00 | 0.05 | 0.13 | 0.02 | 0.06 | 0.04 | 0.07 | 0.01 | 0.16 | 0.00 | 0.07 | 0.02 | 0.01 | 0.01 | 0.01 | 0.02 | 0.02 | 0.01 | 0.03 | 0.04 | 0.05 | 0.11 | 0.06 | 0.05 | 0.01 | 0.01 | 0.00 | 0.00 | 0.11 | 0.02 | 0.09 | 0.12 | 0.03 | 0.01 | 0.03 | 0.01 | 0.00 | 0.03 | 0.03 | 0.09 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.00 | 0.01 | 0.02 | 0.00 | 0.04 | 0.00 | 0.00 | 0.02 | 0.04 |
| ADAM21 | ENSG00000139985 | 0.01 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.04 | 0.03 | 0.05 | 0.00 | 0.01 | 0.00 | 0.05 | 0.03 | 0.04 | 0.03 | 0.05 | 0.04 | 0.02 | 0.05 | 0.03 | 0.02 | 0.05 | 0.00 | 0.02 | 0.01 | 0.03 | 0.01 | 0.01 | 0.01 | 0.09 | 0.00 | 0.33 | 0.00 | 0.05 | 0.01 | 0.04 | 0.00 | 0.00 | 0.01 | 0.11 | 0.08 | 0.25 | 0.02 | 0.02 | 0.01 | 0.02 | 0.05 | 0.04 | 0.05 | 0.14 | 0.02 | 0.01 | 0.00 | 0.00 | 0.04 | 0.00 | 0.00 | 0.11 | 0.01 | 0.07 | 0.03 | 0.00 | 0.01 | 0.04 |
| RDH12 | ENSG00000139988 | 0.01 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.05 | 0.04 | 0.08 | 0.00 | 0.01 | 0.02 | 0.06 | 0.03 | 0.04 | 0.03 | 0.05 | 0.07 | 0.01 | 0.10 | 0.02 | 0.03 | 0.05 | 0.00 | 0.03 | 0.02 | 0.03 | 0.01 | 0.00 | 0.00 | 0.10 | 0.00 | 0.33 | 0.10 | 0.05 | 0.02 | 0.03 | 0.00 | 0.00 | 0.02 | 0.10 | 0.06 | 0.26 | 0.02 | 0.02 | 0.02 | 0.03 | 0.09 | 0.06 | 0.04 | 0.15 | 0.02 | 0.01 | 0.01 | 0.00 | 0.04 | 0.00 | 0.00 | 0.11 | 0.01 | 0.07 | 0.03 | 0.00 | 0.02 | 0.04 |
| KCNH5 | ENSG00000140015 | 0.00 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.02 | 0.04 | 0.00 | 0.01 | 0.00 | 0.03 | 0.04 | 0.03 | 0.04 | 0.04 | 0.08 | 0.01 | 0.06 | 0.01 | 0.05 | 0.04 | 0.00 | 0.03 | 0.01 | 0.03 | 0.01 | 0.01 | 0.00 | 0.08 | 0.00 | 0.28 | 0.07 | 0.04 | 0.01 | 0.03 | 0.00 | 0.00 | 0.04 | 0.07 | 0.04 | 0.26 | 0.02 | 0.01 | 0.01 | 0.02 | 0.03 | 0.04 | 0.03 | 0.10 | 0.02 | 0.01 | 0.00 | 0.00 | 0.04 | 0.00 | 0.00 | 0.10 | 0.01 | 0.07 | 0.03 | 0.00 | 0.01 | 0.04 |
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