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 |
| DOT1L | ENSG00000104885 | 0.00 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.05 | 0.04 | 0.13 | 0.05 | 0.00 | 0.03 | 0.10 | 0.02 | 0.08 | 0.02 | 0.13 | 0.02 | 0.14 | 0.04 | 0.17 | 0.02 | 0.09 | 0.01 | 0.05 | 0.01 | 0.09 | 0.00 | 0.07 | 0.04 | 0.13 | 0.00 | 0.03 | 0.11 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.02 | 0.16 | 0.03 | 0.90 | 0.08 | 0.20 | 0.02 | 0.27 | 0.02 | 0.80 | 0.17 | 0.15 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.07 | 0.03 | 0.02 | 0.07 | 0.01 | 0.02 | 0.02 | 0.03 | 0.07 |
| GSTM4 | ENSG00000168765 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.05 | 0.09 | 0.06 | 0.00 | 0.00 | 0.00 | 0.33 | 0.01 | 0.13 | 0.01 | 0.14 | 0.00 | 0.12 | 0.06 | 0.12 | 0.03 | 0.07 | 0.00 | 0.06 | 0.00 | 0.07 | 0.00 | 0.02 | 0.03 | 0.03 | 0.00 | 0.11 | 0.05 | 0.04 | 0.00 | 0.26 | 0.00 | 0.00 | 0.04 | 0.10 | 0.17 | 0.15 | 0.01 | 0.08 | 0.04 | 0.03 | 0.13 | 0.06 | 0.05 | 0.10 | 0.03 | 0.04 | 0.00 | 0.00 | 0.00 | 0.05 | 0.01 | 0.01 | 0.01 | 0.02 | 0.00 | 0.03 | 0.07 | 0.10 |
| SCGN | ENSG00000079689 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.01 | 0.28 | 0.02 | 0.00 | 0.01 | 0.02 | 0.03 | 0.07 | 0.02 | 0.07 | 0.06 | 0.02 | 0.05 | 0.10 | 0.13 | 0.04 | 0.05 | 0.04 | 0.04 | 0.04 | 0.03 | 0.03 | 0.03 | 0.11 | 0.01 | 0.06 | 0.08 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.13 | 0.03 | 0.38 | 0.06 | 0.09 | 0.04 | 0.05 | 0.01 | 0.20 | 0.02 | 0.06 | 0.08 | 0.01 | 0.02 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.02 | 0.02 | 0.00 | 0.16 | 0.00 | 0.16 | 0.01 |
| AZGP1 | ENSG00000160862 | 0.01 | 0.00 | 0.06 | 0.00 | 0.00 | 0.00 | 0.04 | 0.02 | 0.08 | 0.01 | 0.00 | 0.00 | 0.03 | 0.00 | 0.12 | 0.02 | 0.24 | 0.02 | 0.24 | 0.00 | 0.52 | 0.02 | 0.36 | 0.01 | 0.02 | 0.01 | 0.02 | 0.00 | 0.10 | 0.01 | 0.08 | 0.01 | 0.11 | 0.01 | 0.10 | 0.03 | 0.00 | 0.02 | 0.00 | 0.00 | 0.07 | 0.03 | 0.21 | 0.05 | 0.07 | 0.01 | 0.11 | 0.01 | 0.24 | 0.03 | 0.07 | 0.03 | 0.09 | 0.01 | 0.00 | 0.00 | 0.13 | 0.00 | 0.06 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.04 | 0.03 |
| ADAM15 | ENSG00000143537 | 0.03 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.07 | 0.01 | 0.36 | 0.01 | 0.02 | 0.00 | 0.11 | 0.00 | 0.38 | 0.00 | 0.25 | 0.00 | 0.06 | 0.00 | 0.21 | 0.00 | 0.16 | 0.00 | 0.03 | 0.00 | 0.11 | 0.00 | 0.09 | 0.00 | 0.43 | 0.00 | 0.53 | 0.01 | 0.28 | 0.00 | 0.07 | 0.00 | 0.00 | 0.00 | 0.37 | 0.00 | 0.53 | 0.02 | 0.20 | 0.01 | 0.21 | 0.00 | 0.77 | 0.00 | 0.34 | 0.01 | 0.09 | 0.00 | 0.00 | 0.00 | 0.25 | 0.00 | 0.02 | 0.00 | 0.06 | 0.00 | 0.00 | 0.00 | 0.20 | 0.00 |
| KLHL26 | ENSG00000167487 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.03 | 0.01 | 0.04 | 0.07 | 0.00 | 0.03 | 0.03 | 0.11 | 0.02 | 0.05 | 0.02 | 0.13 | 0.01 | 0.03 | 0.02 | 0.00 | 0.00 | 0.01 | 0.04 | 0.02 | 0.02 | 0.09 | 0.02 | 0.06 | 0.03 | 0.18 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.09 | 0.02 | 0.51 | 0.05 | 0.02 | 0.02 | 0.18 | 0.04 | 0.46 | 0.07 | 0.07 | 0.03 | 0.01 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.02 | 0.00 | 0.02 | 0.01 | 0.02 | 0.00 | 0.03 | 0.01 |
| PDZD2 | ENSG00000133401 | 0.00 | 0.00 | 0.01 | 0.01 | 0.06 | 0.03 | 0.02 | 0.01 | 0.09 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.18 | 0.01 | 0.21 | 0.01 | 0.06 | 0.00 | 0.10 | 0.01 | 0.13 | 0.03 | 0.04 | 0.01 | 0.03 | 0.01 | 0.02 | 0.00 | 0.06 | 0.00 | 0.00 | 0.01 | 0.28 | 0.02 | 0.01 | 0.01 | 0.00 | 0.00 | 0.06 | 0.03 | 0.19 | 0.03 | 0.06 | 0.00 | 0.08 | 0.01 | 0.18 | 0.03 | 0.25 | 0.02 | 0.00 | 0.02 | 0.00 | 0.01 | 0.02 | 0.00 | 0.01 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.15 | 0.04 |
| DUSP7 | ENSG00000164086 | 0.00 | 0.18 | 0.00 | 0.02 | 0.00 | 0.02 | 0.00 | 0.03 | 0.03 | 0.15 | 0.00 | 0.01 | 0.00 | 0.55 | 0.01 | 0.06 | 0.00 | 0.11 | 0.00 | 0.06 | 0.00 | 0.13 | 0.00 | 0.10 | 0.00 | 0.06 | 0.01 | 0.08 | 0.00 | 0.04 | 0.04 | 0.06 | 0.00 | 0.20 | 0.05 | 0.02 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.17 | 0.08 | 0.21 | 0.01 | 0.07 | 0.08 | 0.06 | 0.03 | 0.29 | 0.04 | 0.15 | 0.05 | 0.01 | 0.00 | 0.01 | 0.00 | 0.06 | 0.00 | 0.06 | 0.02 | 0.04 | 0.00 | 0.03 | 0.02 | 0.05 |
| BGN | ENSG00000182492 | 0.03 | 0.01 | 0.02 | 0.00 | 0.01 | 0.00 | 0.02 | 0.00 | 0.11 | 0.04 | 0.06 | 0.00 | 0.06 | 0.01 | 0.23 | 0.01 | 0.18 | 0.02 | 0.15 | 0.01 | 0.23 | 0.01 | 0.17 | 0.02 | 0.05 | 0.00 | 0.10 | 0.01 | 0.07 | 0.00 | 0.12 | 0.03 | 0.10 | 0.01 | 0.28 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.10 | 0.02 | 0.43 | 0.09 | 0.21 | 0.02 | 0.10 | 0.03 | 0.17 | 0.07 | 0.22 | 0.07 | 0.01 | 0.02 | 0.00 | 0.00 | 0.15 | 0.07 | 0.02 | 0.03 | 0.03 | 0.01 | 0.05 | 0.00 | 0.06 | 0.01 |
| MLLT10 | ENSG00000078403 | 0.00 | 0.01 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.05 | 0.05 | 0.00 | 0.00 | 0.02 | 0.02 | 0.03 | 0.03 | 0.03 | 0.07 | 0.02 | 0.03 | 0.05 | 0.02 | 0.06 | 0.04 | 0.01 | 0.02 | 0.01 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 | 0.00 | 0.01 | 0.03 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.02 | 0.17 | 0.05 | 0.01 | 0.01 | 0.03 | 0.02 | 0.16 | 0.00 | 0.07 | 0.06 | 0.01 | 0.00 | 0.01 | 0.01 | 0.00 | 0.03 | 0.02 | 0.02 | 0.03 | 0.02 | 0.00 | 0.00 | 0.02 | 0.02 |
| SUV420H1 | ENSG00000110066 | 0.01 | 0.00 | 0.03 | 0.01 | 0.08 | 0.02 | 0.10 | 0.01 | 0.28 | 0.01 | 0.00 | 0.00 | 0.08 | 0.00 | 0.15 | 0.01 | 0.22 | 0.02 | 0.41 | 0.02 | 0.70 | 0.03 | 0.16 | 0.03 | 0.02 | 0.01 | 0.03 | 0.02 | 0.03 | 0.01 | 0.21 | 0.02 | 0.19 | 0.01 | 0.03 | 0.03 | 0.03 | 0.00 | 0.00 | 0.00 | 0.45 | 0.04 | 0.29 | 0.03 | 0.20 | 0.01 | 0.17 | 0.02 | 0.22 | 0.10 | 0.11 | 0.03 | 0.00 | 0.05 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.01 | 0.02 | 0.04 | 0.00 | 0.00 | 0.28 | 0.01 |
| ALDH1A2 | ENSG00000128918 | 0.00 | 0.00 | 0.00 | 0.01 | 0.14 | 0.02 | 0.01 | 0.05 | 0.06 | 0.05 | 0.00 | 0.00 | 0.08 | 0.07 | 0.02 | 0.04 | 0.04 | 0.04 | 0.01 | 0.02 | 0.03 | 0.03 | 0.03 | 0.05 | 0.01 | 0.03 | 0.00 | 0.07 | 0.01 | 0.02 | 0.08 | 0.02 | 0.00 | 0.01 | 0.04 | 0.05 | 0.00 | 0.02 | 0.00 | 0.00 | 0.03 | 0.07 | 0.06 | 0.15 | 0.03 | 0.07 | 0.01 | 0.08 | 0.06 | 0.26 | 0.11 | 0.03 | 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 | 0.07 |
| FAAH2 | ENSG00000165591 | 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 | 0.02 | 0.05 | 0.02 | 0.04 | 0.03 | 0.06 | 0.02 | 0.12 | 0.04 | 0.03 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.00 | 0.01 | 0.07 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.07 | 0.01 | 0.23 | 0.03 | 0.04 | 0.03 | 0.08 | 0.01 | 0.28 | 0.04 | 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 | 0.01 | 0.00 |
| CYP4F3 | ENSG00000186529 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.02 | 0.04 | 0.00 | 0.00 | 0.06 | 0.00 | 0.01 | 0.02 | 0.10 | 0.02 | 0.07 | 0.01 | 0.23 | 0.01 | 0.05 | 0.02 | 0.02 | 0.00 | 0.02 | 0.00 | 0.01 | 0.00 | 0.09 | 0.03 | 0.00 | 0.03 | 0.32 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.11 | 0.02 | 0.79 | 0.04 | 0.01 | 0.01 | 0.24 | 0.01 | 0.32 | 0.05 | 0.17 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.02 | 0.00 | 0.03 | 0.00 | 0.02 | 0.00 | 0.02 | 0.02 |
| LBR | ENSG00000143815 | 0.01 | 0.02 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.08 | 0.10 | 0.04 | 0.02 | 0.00 | 0.05 | 0.01 | 0.09 | 0.01 | 0.13 | 0.01 | 0.05 | 0.01 | 0.22 | 0.03 | 0.11 | 0.01 | 0.03 | 0.01 | 0.05 | 0.01 | 0.01 | 0.01 | 0.14 | 0.03 | 0.18 | 0.02 | 0.04 | 0.02 | 0.00 | 0.02 | 0.00 | 0.00 | 0.23 | 0.02 | 0.39 | 0.05 | 0.07 | 0.01 | 0.10 | 0.02 | 0.16 | 0.00 | 0.08 | 0.24 | 0.03 | 0.05 | 0.02 | 0.00 | 0.03 | 0.15 | 0.01 | 0.02 | 0.02 | 0.06 | 0.09 | 0.00 | 0.12 | 0.05 |
| SLC25A42 | ENSG00000181035 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.02 | 0.03 | 0.01 | 0.03 | 0.05 | 0.00 | 0.03 | 0.03 | 0.10 | 0.02 | 0.04 | 0.02 | 0.15 | 0.01 | 0.03 | 0.02 | 0.00 | 0.01 | 0.02 | 0.04 | 0.01 | 0.02 | 0.08 | 0.02 | 0.06 | 0.03 | 0.21 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.09 | 0.02 | 0.53 | 0.06 | 0.03 | 0.02 | 0.17 | 0.03 | 0.37 | 0.05 | 0.07 | 0.05 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.08 | 0.01 | 0.00 | 0.01 | 0.01 | 0.02 | 0.00 | 0.03 | 0.02 |
| CAMKK1 | ENSG00000004660 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.07 | 0.05 | 0.03 | 0.00 | 0.00 | 0.01 | 0.02 | 0.02 | 0.06 | 0.02 | 0.02 | 0.01 | 0.03 | 0.05 | 0.05 | 0.02 | 0.02 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.12 | 0.02 | 0.08 | 0.03 | 0.03 | 0.00 | 0.03 | 0.00 | 0.00 | 0.04 | 0.05 | 0.13 | 0.08 | 0.01 | 0.03 | 0.04 | 0.04 | 0.07 | 0.11 | 0.15 | 0.23 | 0.00 | 0.02 | 0.00 | 0.02 | 0.00 | 0.06 | 0.00 | 0.00 | 0.00 | 0.05 | 0.00 | 0.00 | 0.04 | 0.03 |
| SLC6A15 | ENSG00000072041 | 0.00 | 0.01 | 0.00 | 0.00 | 0.06 | 0.00 | 0.03 | 0.01 | 0.04 | 0.05 | 0.00 | 0.00 | 0.01 | 0.03 | 0.02 | 0.05 | 0.04 | 0.04 | 0.00 | 0.03 | 0.04 | 0.07 | 0.03 | 0.04 | 0.00 | 0.03 | 0.02 | 0.03 | 0.00 | 0.07 | 0.02 | 0.02 | 0.00 | 0.08 | 0.16 | 0.02 | 0.00 | 0.02 | 0.00 | 0.00 | 0.08 | 0.06 | 0.06 | 0.20 | 0.01 | 0.02 | 0.01 | 0.03 | 0.00 | 0.16 | 0.49 | 0.04 | 0.01 | 0.00 | 0.00 | 0.01 | 0.09 | 0.02 | 0.00 | 0.02 | 0.02 | 0.05 | 0.00 | 0.00 | 0.03 | 0.06 |
| CDH5 | ENSG00000179776 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.06 | 0.00 | 0.06 | 0.11 | 0.02 | 0.00 | 0.00 | 0.00 | 0.06 | 0.05 | 0.03 | 0.05 | 0.01 | 0.03 | 0.01 | 0.11 | 0.00 | 0.04 | 0.02 | 0.01 | 0.00 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.04 | 0.05 | 0.01 | 0.22 | 0.03 | 0.01 | 0.02 | 0.00 | 0.01 | 0.02 | 0.05 | 0.03 | 0.28 | 0.02 | 0.04 | 0.03 | 0.07 | 0.05 | 0.14 | 0.02 | 0.06 | 0.15 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.03 | 0.02 | 0.00 |
| MYO3B | ENSG00000071909 | 0.02 | 0.01 | 0.05 | 0.00 | 0.00 | 0.00 | 0.01 | 0.10 | 0.07 | 0.04 | 0.00 | 0.01 | 0.00 | 0.00 | 0.07 | 0.01 | 0.12 | 0.02 | 0.10 | 0.01 | 0.16 | 0.02 | 0.05 | 0.04 | 0.01 | 0.01 | 0.03 | 0.02 | 0.03 | 0.02 | 0.05 | 0.06 | 0.00 | 0.01 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.03 | 0.35 | 0.04 | 0.08 | 0.02 | 0.06 | 0.01 | 0.04 | 0.00 | 0.05 | 0.11 | 0.04 | 0.01 | 0.00 | 0.00 | 0.00 | 0.07 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.02 |
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