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 |
| PIGK | ENSG00000142892 | 0.00 | 0.01 | 0.02 | 0.00 | 0.00 | 0.00 | 0.01 | 0.08 | 0.12 | 0.05 | 0.00 | 0.00 | 0.02 | 0.21 | 0.04 | 0.08 | 0.06 | 0.06 | 0.01 | 0.06 | 0.03 | 0.07 | 0.03 | 0.06 | 0.00 | 0.08 | 0.02 | 0.07 | 0.00 | 0.01 | 0.02 | 0.04 | 0.00 | 0.08 | 0.04 | 0.02 | 0.00 | 0.20 | 0.00 | 0.00 | 0.06 | 0.07 | 0.12 | 0.15 | 0.03 | 0.03 | 0.01 | 0.02 | 0.07 | 0.06 | 0.19 | 0.04 | 0.04 | 0.02 | 0.02 | 0.01 | 0.00 | 0.03 | 0.00 | 0.01 | 0.01 | 0.03 | 0.03 | 0.05 | 0.02 | 0.09 |
| SLC25A36 | ENSG00000114120 | 0.03 | 0.01 | 0.02 | 0.01 | 0.00 | 0.00 | 0.07 | 0.02 | 0.08 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.06 | 0.01 | 0.44 | 0.01 | 0.25 | 0.00 | 0.30 | 0.01 | 0.11 | 0.02 | 0.01 | 0.00 | 0.05 | 0.00 | 0.00 | 0.00 | 0.05 | 0.01 | 0.00 | 0.03 | 0.09 | 0.01 | 0.00 | 0.05 | 0.00 | 0.00 | 0.10 | 0.02 | 0.51 | 0.03 | 0.29 | 0.00 | 0.10 | 0.00 | 0.23 | 0.02 | 0.10 | 0.07 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.02 | 0.00 | 0.01 | 0.03 | 0.04 | 0.00 | 0.00 | 0.01 | 0.06 |
| NPTN | ENSG00000156642 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.02 | 0.01 | 0.03 | 0.05 | 0.03 | 0.00 | 0.00 | 0.09 | 0.00 | 0.04 | 0.02 | 0.06 | 0.01 | 0.03 | 0.02 | 0.07 | 0.02 | 0.05 | 0.03 | 0.02 | 0.01 | 0.03 | 0.03 | 0.03 | 0.01 | 0.04 | 0.03 | 0.00 | 0.01 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.09 | 0.03 | 0.17 | 0.12 | 0.11 | 0.01 | 0.03 | 0.04 | 0.19 | 0.03 | 0.05 | 0.10 | 0.01 | 0.01 | 0.00 | 0.00 | 0.06 | 0.00 | 0.01 | 0.01 | 0.01 | 0.02 | 0.00 | 0.00 | 0.16 | 0.01 |
| PRDM5 | ENSG00000138738 | 0.00 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.08 | 0.05 | 0.06 | 0.00 | 0.00 | 0.00 | 0.05 | 0.02 | 0.05 | 0.03 | 0.07 | 0.03 | 0.03 | 0.01 | 0.04 | 0.02 | 0.06 | 0.01 | 0.03 | 0.01 | 0.04 | 0.00 | 0.02 | 0.03 | 0.06 | 0.00 | 0.11 | 0.11 | 0.05 | 0.00 | 0.01 | 0.00 | 0.00 | 0.05 | 0.04 | 0.04 | 0.25 | 0.01 | 0.04 | 0.01 | 0.04 | 0.04 | 0.07 | 0.05 | 0.09 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.05 | 0.01 | 0.04 | 0.00 | 0.01 | 0.00 | 0.00 | 0.03 | 0.04 |
| LPO | ENSG00000167419 | 0.01 | 0.00 | 0.05 | 0.00 | 0.00 | 0.00 | 0.02 | 0.05 | 0.17 | 0.02 | 0.02 | 0.00 | 0.11 | 0.00 | 0.10 | 0.01 | 0.14 | 0.02 | 0.04 | 0.03 | 0.15 | 0.05 | 0.05 | 0.03 | 0.04 | 0.01 | 0.07 | 0.04 | 0.01 | 0.15 | 0.16 | 0.00 | 0.12 | 0.01 | 0.14 | 0.03 | 0.02 | 0.00 | 0.00 | 0.00 | 0.48 | 0.02 | 0.16 | 0.03 | 0.10 | 0.01 | 0.09 | 0.03 | 0.19 | 0.02 | 0.19 | 0.03 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.06 | 0.00 | 0.04 | 0.00 | 0.17 | 0.00 | 0.20 | 0.02 |
| LAP3 | ENSG00000002549 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.01 | 0.03 | 0.04 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.02 | 0.02 | 0.07 | 0.02 | 0.05 | 0.04 | 0.05 | 0.03 | 0.03 | 0.01 | 0.01 | 0.03 | 0.03 | 0.00 | 0.02 | 0.04 | 0.03 | 0.00 | 0.01 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.04 | 0.16 | 0.06 | 0.01 | 0.01 | 0.04 | 0.03 | 0.11 | 0.00 | 0.11 | 0.04 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.01 | 0.02 | 0.05 | 0.00 | 0.07 | 0.01 |
| RHD | ENSG00000187010 | 0.00 | 0.06 | 0.00 | 0.08 | 0.00 | 0.00 | 0.01 | 0.03 | 0.07 | 0.08 | 0.00 | 0.03 | 0.05 | 0.21 | 0.04 | 0.06 | 0.02 | 0.12 | 0.03 | 0.07 | 0.03 | 0.11 | 0.02 | 0.12 | 0.00 | 0.16 | 0.00 | 0.21 | 0.01 | 0.08 | 0.02 | 0.22 | 0.00 | 1.06 | 0.01 | 0.10 | 0.01 | 0.07 | 0.00 | 0.00 | 0.02 | 0.18 | 0.10 | 0.45 | 0.04 | 0.08 | 0.03 | 0.11 | 0.00 | 0.18 | 0.15 | 0.09 | 0.05 | 0.05 | 0.02 | 0.00 | 0.00 | 0.11 | 0.00 | 0.02 | 0.02 | 0.08 | 0.00 | 0.12 | 0.07 | 0.06 |
| SENP1 | ENSG00000079387 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.07 | 0.03 | 0.00 | 0.00 | 0.00 | 0.06 | 0.06 | 0.02 | 0.07 | 0.02 | 0.02 | 0.04 | 0.05 | 0.05 | 0.07 | 0.04 | 0.02 | 0.01 | 0.02 | 0.02 | 0.00 | 0.04 | 0.01 | 0.01 | 0.09 | 0.01 | 0.23 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.05 | 0.05 | 0.13 | 0.06 | 0.03 | 0.00 | 0.10 | 0.02 | 0.24 | 0.15 | 0.16 | 0.08 | 0.02 | 0.00 | 0.00 | 0.01 | 0.13 | 0.03 | 0.01 | 0.04 | 0.01 | 0.05 | 0.00 | 0.00 | 0.07 | 0.04 |
| CRAT | ENSG00000095321 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.03 | 0.02 | 0.00 | 0.01 | 0.00 | 0.02 | 0.05 | 0.03 | 0.05 | 0.03 | 0.07 | 0.02 | 0.11 | 0.03 | 0.11 | 0.02 | 0.01 | 0.01 | 0.04 | 0.03 | 0.00 | 0.01 | 0.04 | 0.03 | 0.06 | 0.01 | 0.07 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.05 | 0.09 | 0.21 | 0.04 | 0.01 | 0.03 | 0.06 | 0.07 | 0.11 | 0.08 | 0.11 | 0.02 | 0.04 | 0.01 | 0.00 | 0.05 | 0.00 | 0.02 | 0.01 | 0.04 | 0.02 | 0.00 | 0.00 | 0.03 | 0.02 |
| PDE11A | ENSG00000128655 | 0.02 | 0.01 | 0.07 | 0.00 | 0.00 | 0.00 | 0.01 | 0.08 | 0.06 | 0.05 | 0.00 | 0.00 | 0.00 | 0.00 | 0.07 | 0.01 | 0.21 | 0.02 | 0.19 | 0.01 | 0.20 | 0.01 | 0.04 | 0.05 | 0.01 | 0.01 | 0.03 | 0.02 | 0.03 | 0.01 | 0.07 | 0.04 | 0.05 | 0.01 | 0.02 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.06 | 0.03 | 0.49 | 0.05 | 0.13 | 0.02 | 0.08 | 0.01 | 0.07 | 0.00 | 0.04 | 0.10 | 0.04 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.02 | 0.03 |
| MAPK8 | ENSG00000107643 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.05 | 0.09 | 0.07 | 0.00 | 0.00 | 0.01 | 0.04 | 0.05 | 0.03 | 0.07 | 0.03 | 0.04 | 0.03 | 0.08 | 0.09 | 0.03 | 0.02 | 0.00 | 0.03 | 0.00 | 0.01 | 0.00 | 0.01 | 0.01 | 0.02 | 0.09 | 0.01 | 0.02 | 0.07 | 0.00 | 0.00 | 0.00 | 0.01 | 0.05 | 0.04 | 0.11 | 0.14 | 0.01 | 0.04 | 0.02 | 0.04 | 0.05 | 0.06 | 0.09 | 0.10 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.01 | 0.01 | 0.02 | 0.00 | 0.00 | 0.00 | 0.03 |
| GABRA2 | ENSG00000151834 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.01 | 0.04 | 0.03 | 0.02 | 0.00 | 0.00 | 0.00 | 0.03 | 0.08 | 0.02 | 0.10 | 0.03 | 0.03 | 0.02 | 0.10 | 0.02 | 0.03 | 0.03 | 0.00 | 0.01 | 0.02 | 0.03 | 0.01 | 0.01 | 0.04 | 0.00 | 0.00 | 0.07 | 0.04 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.02 | 0.13 | 0.04 | 0.00 | 0.03 | 0.04 | 0.01 | 0.10 | 0.07 | 0.08 | 0.03 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.01 | 0.05 | 0.00 | 0.03 | 0.01 |
| CA1 | ENSG00000133742 | 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 | 0.15 | 0.02 | 0.14 | 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 | 0.28 | 0.12 | 0.05 | 0.01 | 0.04 | 0.01 | 0.19 | 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 |
| SLC41A3 | ENSG00000114544 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.03 | 0.05 | 0.02 | 0.00 | 0.01 | 0.00 | 0.01 | 0.04 | 0.01 | 0.11 | 0.02 | 0.05 | 0.00 | 0.10 | 0.04 | 0.06 | 0.02 | 0.00 | 0.00 | 0.04 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 | 0.00 | 0.05 | 0.03 | 0.02 | 0.00 | 0.05 | 0.00 | 0.00 | 0.03 | 0.03 | 0.24 | 0.04 | 0.08 | 0.00 | 0.05 | 0.00 | 0.09 | 0.09 | 0.06 | 0.06 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.03 | 0.01 | 0.06 | 0.00 | 0.00 | 0.00 | 0.04 |
| STK19 | ENSG00000204344 | 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 |
| USP1 | ENSG00000162607 | 0.00 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.06 | 0.07 | 0.05 | 0.00 | 0.02 | 0.06 | 0.01 | 0.08 | 0.06 | 0.07 | 0.04 | 0.06 | 0.03 | 0.08 | 0.05 | 0.04 | 0.04 | 0.00 | 0.06 | 0.00 | 0.05 | 0.00 | 0.01 | 0.02 | 0.05 | 0.00 | 0.13 | 0.04 | 0.03 | 0.01 | 0.17 | 0.00 | 0.00 | 0.09 | 0.06 | 0.23 | 0.13 | 0.09 | 0.02 | 0.04 | 0.02 | 0.00 | 0.07 | 0.23 | 0.03 | 0.03 | 0.05 | 0.02 | 0.01 | 0.00 | 0.03 | 0.00 | 0.01 | 0.02 | 0.01 | 0.00 | 0.07 | 0.04 | 0.03 |
| PHF8 | ENSG00000172943 | 0.01 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.03 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.07 | 0.03 | 0.03 | 0.03 | 0.05 | 0.03 | 0.02 | 0.01 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.13 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.08 | 0.01 | 0.25 | 0.04 | 0.02 | 0.03 | 0.06 | 0.01 | 0.27 | 0.06 | 0.17 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.07 | 0.00 | 0.08 | 0.00 | 0.03 | 0.00 | 0.03 | 0.00 | 0.02 | 0.00 |
| SMYD5 | ENSG00000135632 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.03 | 0.11 | 0.01 | 0.00 | 0.00 | 0.00 | 0.05 | 0.03 | 0.01 | 0.13 | 0.01 | 0.04 | 0.00 | 0.07 | 0.01 | 0.03 | 0.01 | 0.00 | 0.01 | 0.01 | 0.01 | 0.00 | 0.01 | 0.02 | 0.02 | 0.00 | 0.02 | 0.03 | 0.02 | 0.01 | 0.01 | 0.00 | 0.00 | 0.05 | 0.01 | 0.15 | 0.04 | 0.03 | 0.00 | 0.04 | 0.01 | 0.10 | 0.02 | 0.06 | 0.05 | 0.03 | 0.04 | 0.00 | 0.00 | 0.04 | 0.02 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.01 |
| ADAM10 | ENSG00000137845 | 0.00 | 0.00 | 0.00 | 0.01 | 0.14 | 0.02 | 0.01 | 0.04 | 0.03 | 0.06 | 0.00 | 0.00 | 0.08 | 0.07 | 0.02 | 0.04 | 0.03 | 0.04 | 0.02 | 0.03 | 0.04 | 0.03 | 0.03 | 0.05 | 0.01 | 0.03 | 0.00 | 0.07 | 0.01 | 0.02 | 0.04 | 0.01 | 0.00 | 0.01 | 0.04 | 0.03 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.07 | 0.05 | 0.15 | 0.02 | 0.05 | 0.01 | 0.07 | 0.06 | 0.26 | 0.10 | 0.02 | 0.01 | 0.02 | 0.00 | 0.00 | 0.06 | 0.02 | 0.01 | 0.03 | 0.01 | 0.06 | 0.00 | 0.00 | 0.04 | 0.06 |
| PARP6 | ENSG00000137817 | 0.01 | 0.00 | 0.01 | 0.00 | 0.02 | 0.02 | 0.01 | 0.02 | 0.05 | 0.02 | 0.00 | 0.00 | 0.09 | 0.02 | 0.04 | 0.01 | 0.06 | 0.01 | 0.04 | 0.02 | 0.07 | 0.02 | 0.08 | 0.02 | 0.03 | 0.00 | 0.01 | 0.03 | 0.03 | 0.01 | 0.02 | 0.02 | 0.00 | 0.01 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.09 | 0.03 | 0.24 | 0.09 | 0.10 | 0.01 | 0.05 | 0.04 | 0.13 | 0.01 | 0.07 | 0.08 | 0.01 | 0.01 | 0.00 | 0.00 | 0.06 | 0.00 | 0.01 | 0.01 | 0.02 | 0.01 | 0.00 | 0.00 | 0.12 | 0.00 |
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