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 |
| SLC2A8 | ENSG00000136856 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.05 | 0.00 | 0.03 | 0.03 | 0.00 | 0.01 | 0.00 | 0.02 | 0.04 | 0.02 | 0.06 | 0.02 | 0.05 | 0.01 | 0.13 | 0.02 | 0.09 | 0.01 | 0.01 | 0.01 | 0.04 | 0.02 | 0.00 | 0.01 | 0.03 | 0.04 | 0.07 | 0.04 | 0.12 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.09 | 0.03 | 0.10 | 0.17 | 0.04 | 0.01 | 0.05 | 0.04 | 0.11 | 0.19 | 0.06 | 0.07 | 0.02 | 0.04 | 0.01 | 0.00 | 0.05 | 0.00 | 0.02 | 0.00 | 0.03 | 0.02 | 0.00 | 0.00 | 0.03 | 0.02 |
| CSNK1G3 | ENSG00000151292 | 0.25 | 0.01 | 0.03 | 0.01 | 0.02 | 0.00 | 0.02 | 0.07 | 0.02 | 0.07 | 0.00 | 0.00 | 0.00 | 0.08 | 0.01 | 0.07 | 0.00 | 0.06 | 0.00 | 0.06 | 0.02 | 0.07 | 0.02 | 0.13 | 0.01 | 0.08 | 0.01 | 0.07 | 0.00 | 0.04 | 0.07 | 0.03 | 0.05 | 0.02 | 0.23 | 0.02 | 0.00 | 0.03 | 0.01 | 0.00 | 0.02 | 0.05 | 0.09 | 0.29 | 0.00 | 0.03 | 0.02 | 0.03 | 0.07 | 0.06 | 0.04 | 0.05 | 0.01 | 0.00 | 0.00 | 0.09 | 0.04 | 0.02 | 0.00 | 0.03 | 0.01 | 0.02 | 0.00 | 0.03 | 0.06 | 0.08 |
| NEK4 | ENSG00000114904 | 0.00 | 0.18 | 0.00 | 0.03 | 0.00 | 0.02 | 0.00 | 0.03 | 0.04 | 0.16 | 0.00 | 0.03 | 0.00 | 0.57 | 0.01 | 0.07 | 0.00 | 0.11 | 0.00 | 0.06 | 0.04 | 0.13 | 0.01 | 0.11 | 0.00 | 0.06 | 0.02 | 0.07 | 0.00 | 0.04 | 0.03 | 0.07 | 0.00 | 0.20 | 0.06 | 0.01 | 0.00 | 0.04 | 0.00 | 0.00 | 0.01 | 0.17 | 0.08 | 0.22 | 0.00 | 0.07 | 0.05 | 0.08 | 0.00 | 0.32 | 0.04 | 0.15 | 0.05 | 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 |
| BRPF3 | ENSG00000096070 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.01 | 0.07 | 0.04 | 0.00 | 0.00 | 0.02 | 0.01 | 0.08 | 0.01 | 0.03 | 0.05 | 0.02 | 0.03 | 0.15 | 0.04 | 0.07 | 0.03 | 0.02 | 0.01 | 0.06 | 0.01 | 0.01 | 0.01 | 0.05 | 0.04 | 0.05 | 0.03 | 0.21 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.07 | 0.03 | 0.26 | 0.05 | 0.08 | 0.00 | 0.06 | 0.01 | 0.22 | 0.07 | 0.07 | 0.07 | 0.05 | 0.01 | 0.00 | 0.00 | 0.08 | 0.00 | 0.01 | 0.00 | 0.02 | 0.00 | 0.10 | 0.00 | 0.09 | 0.01 |
| ADAM18 | ENSG00000168619 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.08 | 0.37 | 0.06 | 0.00 | 0.00 | 0.04 | 0.00 | 0.20 | 0.04 | 0.60 | 0.03 | 0.20 | 0.02 | 0.34 | 0.05 | 0.05 | 0.04 | 0.16 | 0.03 | 0.13 | 0.07 | 0.05 | 0.00 | 0.06 | 0.06 | 0.06 | 0.11 | 0.09 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.54 | 0.04 | 0.23 | 0.09 | 0.07 | 0.03 | 0.14 | 0.03 | 0.61 | 0.14 | 0.18 | 0.04 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.01 | 0.04 | 0.03 |
| MAPK14 | ENSG00000112062 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.01 | 0.07 | 0.04 | 0.00 | 0.00 | 0.02 | 0.01 | 0.08 | 0.01 | 0.03 | 0.05 | 0.02 | 0.03 | 0.17 | 0.04 | 0.07 | 0.03 | 0.03 | 0.01 | 0.05 | 0.01 | 0.05 | 0.01 | 0.06 | 0.03 | 0.05 | 0.03 | 0.07 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.07 | 0.03 | 0.25 | 0.05 | 0.08 | 0.00 | 0.05 | 0.01 | 0.22 | 0.07 | 0.10 | 0.07 | 0.05 | 0.01 | 0.00 | 0.00 | 0.08 | 0.00 | 0.01 | 0.00 | 0.02 | 0.01 | 0.10 | 0.00 | 0.09 | 0.01 |
| NUCB1 | ENSG00000104805 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.04 | 0.08 | 0.04 | 0.00 | 0.02 | 0.00 | 0.06 | 0.01 | 0.08 | 0.04 | 0.10 | 0.02 | 0.02 | 0.05 | 0.05 | 0.06 | 0.03 | 0.01 | 0.03 | 0.01 | 0.03 | 0.03 | 0.05 | 0.05 | 0.03 | 0.00 | 0.07 | 0.19 | 0.02 | 0.00 | 0.03 | 0.00 | 0.00 | 0.08 | 0.05 | 0.05 | 0.33 | 0.05 | 0.07 | 0.03 | 0.06 | 0.21 | 0.19 | 0.04 | 0.18 | 0.00 | 0.04 | 0.01 | 0.01 | 0.07 | 0.05 | 0.00 | 0.14 | 0.01 | 0.13 | 0.00 | 0.00 | 0.02 | 0.02 |
| IMPA1 | ENSG00000133731 | 0.01 | 0.00 | 0.01 | 0.00 | 0.06 | 0.00 | 0.10 | 0.00 | 0.17 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.22 | 0.01 | 0.13 | 0.03 | 0.05 | 0.00 | 0.10 | 0.00 | 0.11 | 0.01 | 0.11 | 0.00 | 0.16 | 0.01 | 0.01 | 0.01 | 0.11 | 0.00 | 0.19 | 0.01 | 0.06 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.25 | 0.01 | 0.24 | 0.11 | 0.04 | 0.01 | 0.05 | 0.01 | 0.15 | 0.02 | 0.19 | 0.05 | 0.14 | 0.00 | 0.00 | 0.00 | 0.08 | 0.00 | 0.02 | 0.01 | 0.00 | 0.01 | 0.22 | 0.00 | 0.12 | 0.01 |
| HSD17B11 | ENSG00000198189 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.03 | 0.03 | 0.13 | 0.05 | 0.00 | 0.00 | 0.00 | 0.06 | 0.02 | 0.03 | 0.06 | 0.04 | 0.05 | 0.02 | 0.05 | 0.07 | 0.02 | 0.07 | 0.01 | 0.02 | 0.00 | 0.01 | 0.00 | 0.01 | 0.03 | 0.11 | 0.00 | 0.03 | 0.09 | 0.02 | 0.02 | 0.02 | 0.00 | 0.00 | 0.04 | 0.04 | 0.05 | 0.23 | 0.01 | 0.03 | 0.02 | 0.02 | 0.02 | 0.09 | 0.05 | 0.07 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.05 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.04 |
| CASK | ENSG00000147044 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.04 | 0.02 | 0.00 | 0.00 | 0.00 | 0.05 | 0.06 | 0.02 | 0.03 | 0.06 | 0.01 | 0.05 | 0.05 | 0.06 | 0.03 | 0.02 | 0.00 | 0.00 | 0.03 | 0.01 | 0.00 | 0.02 | 0.03 | 0.00 | 0.00 | 0.01 | 0.12 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.02 | 0.10 | 0.10 | 0.00 | 0.03 | 0.01 | 0.02 | 0.29 | 0.06 | 0.12 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.06 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 |
| KAT7 | ENSG00000136504 | 0.00 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.12 | 0.01 | 0.00 | 0.00 | 0.09 | 0.00 | 0.10 | 0.00 | 0.10 | 0.01 | 0.02 | 0.01 | 0.19 | 0.01 | 0.09 | 0.01 | 0.03 | 0.01 | 0.06 | 0.04 | 0.04 | 0.02 | 0.05 | 0.01 | 0.02 | 0.01 | 0.04 | 0.04 | 0.01 | 0.04 | 0.00 | 0.00 | 0.47 | 0.03 | 0.16 | 0.04 | 0.06 | 0.00 | 0.06 | 0.03 | 0.18 | 0.02 | 0.13 | 0.05 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.02 | 0.01 | 0.03 | 0.03 | 0.12 | 0.01 |
| CAMK2D | ENSG00000145349 | 0.00 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.06 | 0.03 | 0.07 | 0.00 | 0.00 | 0.00 | 0.06 | 0.02 | 0.04 | 0.02 | 0.05 | 0.03 | 0.02 | 0.04 | 0.04 | 0.02 | 0.05 | 0.01 | 0.04 | 0.00 | 0.02 | 0.00 | 0.02 | 0.03 | 0.10 | 0.00 | 0.11 | 0.12 | 0.02 | 0.03 | 0.01 | 0.00 | 0.00 | 0.04 | 0.06 | 0.06 | 0.28 | 0.01 | 0.02 | 0.02 | 0.04 | 0.01 | 0.11 | 0.04 | 0.06 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.05 | 0.00 | 0.03 | 0.01 | 0.02 | 0.00 | 0.00 | 0.02 | 0.05 |
| FKBP3 | ENSG00000100442 | 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 | 0.13 | 0.03 | 0.05 | 0.08 | 0.05 | 0.02 | 0.10 | 0.04 | 0.05 | 0.05 | 0.01 | 0.03 | 0.01 | 0.02 | 0.01 | 0.01 | 0.04 | 0.03 | 0.10 | 0.02 | 0.09 | 0.05 | 0.01 | 0.01 | 0.00 | 0.00 | 0.07 | 0.04 | 0.12 | 0.10 | 0.02 | 0.01 | 0.01 | 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 |
| SMPD1 | ENSG00000166311 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.03 | 0.01 | 0.01 | 0.00 | 0.10 | 0.00 | 0.00 | 0.02 | 0.08 | 0.01 | 0.06 | 0.02 | 0.14 | 0.01 | 0.06 | 0.05 | 0.09 | 0.02 | 0.04 | 0.01 | 0.01 | 0.01 | 0.02 | 0.00 | 0.05 | 0.05 | 0.02 | 0.03 | 0.01 | 0.01 | 0.07 | 0.02 | 0.07 | 0.00 | 0.00 | 0.02 | 0.10 | 0.01 | 0.41 | 0.01 | 0.05 | 0.02 | 0.07 | 0.03 | 0.09 | 0.03 | 0.13 | 0.02 | 0.00 | 0.00 | 0.00 | 0.05 | 0.00 | 0.01 | 0.09 | 0.01 | 0.05 | 0.00 | 0.00 | 0.01 | 0.03 |
| SPG7 | ENSG00000197912 | 0.00 | 0.00 | 0.01 | 0.04 | 0.00 | 0.06 | 0.01 | 0.23 | 0.08 | 0.06 | 0.00 | 0.00 | 0.02 | 0.19 | 0.01 | 0.12 | 0.04 | 0.07 | 0.03 | 0.05 | 0.08 | 0.05 | 0.05 | 0.05 | 0.02 | 0.03 | 0.03 | 0.04 | 0.02 | 0.01 | 0.02 | 0.08 | 0.05 | 0.05 | 0.07 | 0.06 | 0.00 | 0.02 | 0.00 | 0.01 | 0.05 | 0.10 | 0.08 | 0.35 | 0.05 | 0.07 | 0.01 | 0.09 | 0.03 | 0.29 | 0.09 | 0.07 | 0.00 | 0.12 | 0.00 | 0.04 | 0.03 | 0.00 | 0.00 | 0.02 | 0.01 | 0.05 | 0.00 | 0.06 | 0.02 | 0.11 |
| GFOD2 | ENSG00000141098 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.06 | 0.01 | 0.07 | 0.16 | 0.02 | 0.00 | 0.00 | 0.03 | 0.07 | 0.04 | 0.03 | 0.06 | 0.01 | 0.03 | 0.01 | 0.13 | 0.02 | 0.05 | 0.03 | 0.00 | 0.01 | 0.01 | 0.01 | 0.01 | 0.00 | 0.01 | 0.04 | 0.05 | 0.01 | 0.27 | 0.02 | 0.02 | 0.02 | 0.00 | 0.01 | 0.02 | 0.06 | 0.03 | 0.32 | 0.03 | 0.03 | 0.01 | 0.09 | 0.00 | 0.14 | 0.02 | 0.04 | 0.15 | 0.01 | 0.00 | 0.05 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.03 | 0.00 | 0.03 | 0.05 | 0.01 |
| MANBA | ENSG00000109323 | 0.00 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.02 | 0.04 | 0.05 | 0.00 | 0.00 | 0.00 | 0.06 | 0.02 | 0.03 | 0.03 | 0.05 | 0.01 | 0.02 | 0.03 | 0.06 | 0.02 | 0.03 | 0.01 | 0.03 | 0.01 | 0.03 | 0.00 | 0.01 | 0.01 | 0.13 | 0.00 | 0.03 | 0.04 | 0.07 | 0.04 | 0.01 | 0.00 | 0.00 | 0.06 | 0.05 | 0.03 | 0.31 | 0.02 | 0.01 | 0.01 | 0.04 | 0.00 | 0.11 | 0.02 | 0.05 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.02 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.05 |
| FKBP15 | ENSG00000119321 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.03 | 0.03 | 0.00 | 0.00 | 0.02 | 0.00 | 0.05 | 0.02 | 0.04 | 0.01 | 0.05 | 0.00 | 0.11 | 0.01 | 0.05 | 0.02 | 0.00 | 0.01 | 0.06 | 0.02 | 0.00 | 0.01 | 0.03 | 0.05 | 0.06 | 0.04 | 0.08 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.04 | 0.10 | 0.12 | 0.01 | 0.01 | 0.03 | 0.04 | 0.00 | 0.15 | 0.08 | 0.03 | 0.03 | 0.01 | 0.00 | 0.00 | 0.05 | 0.00 | 0.01 | 0.01 | 0.02 | 0.01 | 0.00 | 0.00 | 0.03 | 0.01 |
| ALCAM | ENSG00000170017 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.02 | 0.03 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.06 | 0.01 | 0.16 | 0.04 | 0.06 | 0.01 | 0.09 | 0.04 | 0.05 | 0.02 | 0.00 | 0.02 | 0.03 | 0.02 | 0.01 | 0.01 | 0.02 | 0.02 | 0.10 | 0.05 | 0.10 | 0.02 | 0.00 | 0.07 | 0.00 | 0.00 | 0.05 | 0.02 | 0.25 | 0.04 | 0.03 | 0.02 | 0.02 | 0.01 | 0.15 | 0.08 | 0.15 | 0.05 | 0.04 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.01 | 0.03 | 0.01 | 0.03 | 0.00 | 0.00 | 0.03 | 0.02 |
| BRD3 | ENSG00000169925 | 0.00 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.03 | 0.01 | 0.04 | 0.03 | 0.00 | 0.01 | 0.05 | 0.02 | 0.05 | 0.03 | 0.08 | 0.02 | 0.07 | 0.03 | 0.12 | 0.04 | 0.12 | 0.01 | 0.02 | 0.01 | 0.05 | 0.03 | 0.01 | 0.00 | 0.08 | 0.03 | 0.06 | 0.01 | 0.12 | 0.04 | 0.02 | 0.01 | 0.00 | 0.00 | 0.05 | 0.06 | 0.07 | 0.25 | 0.07 | 0.01 | 0.01 | 0.06 | 0.03 | 0.14 | 0.05 | 0.15 | 0.03 | 0.06 | 0.01 | 0.00 | 0.05 | 0.00 | 0.02 | 0.01 | 0.03 | 0.04 | 0.00 | 0.00 | 0.03 | 0.02 |
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