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 |
| UBR7 | ENSG00000012963 | 0.00 | 0.02 | 0.01 | 0.01 | 0.00 | 0.04 | 0.01 | 0.04 | 0.04 | 0.06 | 0.00 | 0.00 | 0.00 | 0.05 | 0.04 | 0.05 | 0.10 | 0.02 | 0.05 | 0.05 | 0.07 | 0.06 | 0.04 | 0.05 | 0.00 | 0.03 | 0.01 | 0.02 | 0.01 | 0.01 | 0.01 | 0.10 | 0.00 | 0.31 | 0.05 | 0.00 | 0.03 | 0.01 | 0.00 | 0.00 | 0.04 | 0.09 | 0.19 | 0.17 | 0.07 | 0.09 | 0.05 | 0.03 | 0.10 | 0.04 | 0.06 | 0.09 | 0.03 | 0.01 | 0.00 | 0.00 | 0.03 | 0.00 | 0.00 | 0.10 | 0.01 | 0.06 | 0.03 | 0.01 | 0.01 | 0.06 |
| SMARCC2 | ENSG00000139613 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.08 | 0.03 | 0.00 | 0.00 | 0.02 | 0.02 | 0.12 | 0.01 | 0.04 | 0.01 | 0.01 | 0.02 | 0.12 | 0.03 | 0.15 | 0.02 | 0.02 | 0.00 | 0.02 | 0.01 | 0.02 | 0.01 | 0.05 | 0.01 | 0.00 | 0.01 | 0.17 | 0.03 | 0.06 | 0.00 | 0.00 | 0.00 | 0.05 | 0.04 | 0.30 | 0.04 | 0.04 | 0.00 | 0.19 | 0.00 | 0.55 | 0.04 | 0.16 | 0.07 | 0.01 | 0.00 | 0.00 | 0.00 | 0.12 | 0.00 | 0.01 | 0.03 | 0.05 | 0.05 | 0.00 | 0.00 | 0.05 | 0.03 |
| KCNG2 | ENSG00000178342 | 0.00 | 0.02 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.11 | 0.02 | 0.13 | 0.00 | 0.00 | 0.01 | 0.04 | 0.03 | 0.10 | 0.04 | 0.14 | 0.01 | 0.20 | 0.04 | 0.19 | 0.05 | 0.17 | 0.01 | 0.10 | 0.01 | 0.14 | 0.00 | 0.05 | 0.04 | 0.07 | 0.00 | 0.18 | 0.04 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.09 | 0.09 | 0.44 | 0.03 | 0.06 | 0.04 | 0.10 | 0.12 | 0.12 | 0.16 | 0.14 | 0.00 | 0.10 | 0.00 | 0.02 | 0.08 | 0.05 | 0.01 | 0.06 | 0.02 | 0.05 | 0.00 | 0.04 | 0.02 | 0.03 |
| EPHA5 | ENSG00000145242 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.03 | 0.02 | 0.05 | 0.07 | 0.04 | 0.00 | 0.00 | 0.00 | 0.08 | 0.06 | 0.04 | 0.18 | 0.02 | 0.05 | 0.01 | 0.12 | 0.03 | 0.05 | 0.03 | 0.01 | 0.02 | 0.03 | 0.01 | 0.00 | 0.01 | 0.02 | 0.06 | 0.00 | 0.03 | 0.04 | 0.00 | 0.02 | 0.03 | 0.00 | 0.00 | 0.06 | 0.02 | 0.20 | 0.09 | 0.05 | 0.03 | 0.04 | 0.01 | 0.02 | 0.05 | 0.11 | 0.06 | 0.16 | 0.01 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.02 | 0.00 | 0.03 | 0.00 | 0.00 | 0.02 | 0.03 |
| XPNPEP1 | ENSG00000108039 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.05 | 0.01 | 0.10 | 0.00 | 0.02 | 0.01 | 0.20 | 0.02 | 0.03 | 0.04 | 0.07 | 0.01 | 0.03 | 0.04 | 0.07 | 0.05 | 0.07 | 0.00 | 0.07 | 0.01 | 0.07 | 0.01 | 0.01 | 0.02 | 0.08 | 0.11 | 0.16 | 0.06 | 0.00 | 0.01 | 0.01 | 0.00 | 0.01 | 0.03 | 0.10 | 0.13 | 0.25 | 0.01 | 0.07 | 0.03 | 0.07 | 0.03 | 0.13 | 0.05 | 0.04 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.08 | 0.00 | 0.05 | 0.00 | 0.00 | 0.03 | 0.05 |
| EDEM2 | ENSG00000088298 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.02 | 0.02 | 0.14 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.09 | 0.02 | 0.15 | 0.01 | 0.14 | 0.00 | 0.08 | 0.01 | 0.06 | 0.01 | 0.11 | 0.00 | 0.16 | 0.00 | 0.00 | 0.01 | 0.01 | 0.01 | 0.00 | 0.05 | 0.06 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.16 | 0.02 | 0.17 | 0.03 | 0.14 | 0.00 | 0.05 | 0.01 | 0.32 | 0.00 | 0.12 | 0.03 | 0.00 | 0.01 | 0.00 | 0.03 | 0.01 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.05 | 0.01 |
| GDNF | ENSG00000168621 | 0.00 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.03 | 0.02 | 0.13 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.22 | 0.01 | 0.23 | 0.01 | 0.07 | 0.00 | 0.15 | 0.01 | 0.18 | 0.02 | 0.05 | 0.01 | 0.05 | 0.00 | 0.02 | 0.00 | 0.06 | 0.00 | 0.00 | 0.01 | 0.18 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.07 | 0.02 | 0.21 | 0.02 | 0.07 | 0.00 | 0.06 | 0.00 | 0.15 | 0.03 | 0.24 | 0.03 | 0.00 | 0.00 | 0.00 | 0.01 | 0.05 | 0.00 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.18 | 0.02 |
| CELA3A | ENSG00000142789 | 0.00 | 0.05 | 0.00 | 0.08 | 0.00 | 0.00 | 0.01 | 0.03 | 0.08 | 0.09 | 0.00 | 0.01 | 0.04 | 0.23 | 0.05 | 0.06 | 0.05 | 0.11 | 0.03 | 0.07 | 0.03 | 0.10 | 0.07 | 0.12 | 0.00 | 0.16 | 0.00 | 0.21 | 0.01 | 0.08 | 0.01 | 0.22 | 0.00 | 1.06 | 0.09 | 0.04 | 0.01 | 0.10 | 0.00 | 0.00 | 0.03 | 0.19 | 0.12 | 0.44 | 0.05 | 0.09 | 0.07 | 0.13 | 0.27 | 0.19 | 0.17 | 0.10 | 0.05 | 0.06 | 0.02 | 0.00 | 0.00 | 0.11 | 0.00 | 0.02 | 0.04 | 0.11 | 0.00 | 0.12 | 0.05 | 0.08 |
| MINK1 | ENSG00000141503 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.09 | 0.05 | 0.03 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.05 | 0.02 | 0.02 | 0.02 | 0.03 | 0.06 | 0.05 | 0.03 | 0.01 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.12 | 0.02 | 0.03 | 0.02 | 0.04 | 0.00 | 0.03 | 0.00 | 0.00 | 0.03 | 0.05 | 0.12 | 0.06 | 0.01 | 0.03 | 0.04 | 0.04 | 0.19 | 0.12 | 0.17 | 0.25 | 0.00 | 0.02 | 0.00 | 0.02 | 0.00 | 0.06 | 0.00 | 0.00 | 0.00 | 0.06 | 0.00 | 0.00 | 0.06 | 0.03 |
| AKR1A1 | ENSG00000117448 | 0.00 | 0.02 | 0.01 | 0.03 | 0.00 | 0.00 | 0.00 | 0.02 | 0.10 | 0.03 | 0.00 | 0.00 | 0.08 | 0.03 | 0.09 | 0.02 | 0.08 | 0.02 | 0.07 | 0.02 | 0.04 | 0.02 | 0.04 | 0.03 | 0.02 | 0.02 | 0.02 | 0.02 | 0.01 | 0.01 | 0.02 | 0.09 | 0.00 | 0.23 | 0.04 | 0.03 | 0.01 | 0.11 | 0.00 | 0.00 | 0.06 | 0.04 | 0.41 | 0.06 | 0.09 | 0.00 | 0.09 | 0.01 | 0.11 | 0.03 | 0.11 | 0.04 | 0.06 | 0.04 | 0.02 | 0.00 | 0.04 | 0.03 | 0.00 | 0.01 | 0.02 | 0.00 | 0.00 | 0.07 | 0.05 | 0.02 |
| MAPKAPK5 | ENSG00000089022 | 0.01 | 0.01 | 0.02 | 0.00 | 0.06 | 0.02 | 0.03 | 0.04 | 0.16 | 0.03 | 0.00 | 0.00 | 0.02 | 0.00 | 0.03 | 0.05 | 0.03 | 0.05 | 0.01 | 0.03 | 0.09 | 0.08 | 0.06 | 0.02 | 0.00 | 0.02 | 0.03 | 0.01 | 0.00 | 0.06 | 0.02 | 0.05 | 0.00 | 0.22 | 0.01 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.02 | 0.08 | 0.09 | 0.22 | 0.02 | 0.02 | 0.04 | 0.05 | 0.04 | 0.07 | 0.21 | 0.05 | 0.02 | 0.00 | 0.00 | 0.00 | 0.10 | 0.00 | 0.00 | 0.04 | 0.01 | 0.02 | 0.00 | 0.00 | 0.02 | 0.06 |
| SLC6A4 | ENSG00000108576 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.01 | 0.20 | 0.01 | 0.02 | 0.00 | 0.00 | 0.05 | 0.07 | 0.01 | 0.04 | 0.03 | 0.02 | 0.02 | 0.13 | 0.02 | 0.12 | 0.01 | 0.06 | 0.01 | 0.07 | 0.01 | 0.02 | 0.02 | 0.06 | 0.00 | 0.08 | 0.01 | 0.01 | 0.05 | 0.01 | 0.19 | 0.00 | 0.00 | 0.23 | 0.06 | 0.05 | 0.13 | 0.00 | 0.02 | 0.04 | 0.05 | 0.08 | 0.08 | 0.03 | 0.21 | 0.00 | 0.02 | 0.00 | 0.03 | 0.04 | 0.00 | 0.00 | 0.02 | 0.00 | 0.03 | 0.00 | 0.03 | 0.01 | 0.05 |
| NR2C1 | ENSG00000120798 | 0.01 | 0.01 | 0.00 | 0.00 | 0.06 | 0.02 | 0.05 | 0.01 | 0.07 | 0.05 | 0.00 | 0.00 | 0.02 | 0.03 | 0.02 | 0.05 | 0.03 | 0.03 | 0.02 | 0.04 | 0.04 | 0.06 | 0.02 | 0.03 | 0.00 | 0.02 | 0.01 | 0.04 | 0.02 | 0.06 | 0.03 | 0.03 | 0.00 | 0.17 | 0.00 | 0.01 | 0.01 | 0.03 | 0.00 | 0.00 | 0.06 | 0.07 | 0.06 | 0.22 | 0.01 | 0.03 | 0.02 | 0.04 | 0.05 | 0.14 | 0.24 | 0.05 | 0.00 | 0.01 | 0.00 | 0.02 | 0.08 | 0.05 | 0.00 | 0.02 | 0.00 | 0.02 | 0.05 | 0.00 | 0.02 | 0.08 |
| NELL1 | ENSG00000165973 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.04 | 0.01 | 0.01 | 0.03 | 0.07 | 0.00 | 0.00 | 0.00 | 0.03 | 0.03 | 0.04 | 0.07 | 0.06 | 0.01 | 0.05 | 0.08 | 0.07 | 0.02 | 0.03 | 0.02 | 0.00 | 0.02 | 0.03 | 0.00 | 0.02 | 0.03 | 0.02 | 0.00 | 0.01 | 0.02 | 0.02 | 0.04 | 0.05 | 0.00 | 0.00 | 0.07 | 0.05 | 0.06 | 0.20 | 0.02 | 0.05 | 0.03 | 0.03 | 0.01 | 0.09 | 0.09 | 0.11 | 0.01 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.03 | 0.01 | 0.03 | 0.00 | 0.00 | 0.03 | 0.01 |
| CBX5 | ENSG00000094916 | 0.00 | 0.00 | 0.01 | 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 | 0.01 | 0.02 | 0.07 | 0.03 | 0.08 | 0.03 | 0.02 | 0.00 | 0.02 | 0.02 | 0.01 | 0.02 | 0.02 | 0.01 | 0.17 | 0.01 | 0.20 | 0.01 | 0.05 | 0.00 | 0.00 | 0.00 | 0.04 | 0.05 | 0.21 | 0.06 | 0.04 | 0.00 | 0.08 | 0.01 | 0.20 | 0.09 | 0.17 | 0.08 | 0.01 | 0.00 | 0.00 | 0.00 | 0.09 | 0.00 | 0.00 | 0.04 | 0.04 | 0.05 | 0.00 | 0.00 | 0.03 | 0.04 |
| APPL2 | ENSG00000136044 | 0.01 | 0.01 | 0.02 | 0.00 | 0.06 | 0.02 | 0.04 | 0.03 | 0.06 | 0.04 | 0.00 | 0.00 | 0.04 | 0.02 | 0.02 | 0.05 | 0.03 | 0.04 | 0.01 | 0.03 | 0.04 | 0.05 | 0.05 | 0.04 | 0.00 | 0.01 | 0.02 | 0.03 | 0.00 | 0.06 | 0.03 | 0.04 | 0.00 | 0.22 | 0.00 | 0.02 | 0.01 | 0.03 | 0.00 | 0.00 | 0.03 | 0.08 | 0.07 | 0.22 | 0.02 | 0.01 | 0.03 | 0.04 | 0.02 | 0.11 | 0.15 | 0.05 | 0.00 | 0.01 | 0.00 | 0.00 | 0.10 | 0.00 | 0.01 | 0.03 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.07 |
| SLC9A8 | ENSG00000197818 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.01 | 0.10 | 0.01 | 0.00 | 0.00 | 0.03 | 0.00 | 0.09 | 0.03 | 0.10 | 0.01 | 0.01 | 0.01 | 0.10 | 0.01 | 0.22 | 0.00 | 0.15 | 0.00 | 0.12 | 0.00 | 0.01 | 0.00 | 0.10 | 0.02 | 0.00 | 0.01 | 0.10 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.30 | 0.01 | 0.29 | 0.02 | 0.02 | 0.03 | 0.10 | 0.01 | 0.37 | 0.00 | 0.14 | 0.03 | 0.02 | 0.00 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.13 | 0.00 |
| SETD7 | ENSG00000145391 | 0.01 | 0.02 | 0.00 | 0.01 | 0.06 | 0.00 | 0.02 | 0.02 | 0.05 | 0.09 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.04 | 0.02 | 0.09 | 0.03 | 0.04 | 0.07 | 0.04 | 0.09 | 0.04 | 0.01 | 0.03 | 0.02 | 0.02 | 0.00 | 0.02 | 0.07 | 0.06 | 0.00 | 0.03 | 0.08 | 0.07 | 0.00 | 0.02 | 0.00 | 0.00 | 0.04 | 0.05 | 0.09 | 0.16 | 0.03 | 0.05 | 0.03 | 0.03 | 0.24 | 0.04 | 0.09 | 0.09 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.08 | 0.01 | 0.02 | 0.00 | 0.00 | 0.05 | 0.03 |
| GRIN2B | ENSG00000273079 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.17 | 0.03 | 0.06 | 0.01 | 0.00 | 0.00 | 0.06 | 0.04 | 0.09 | 0.09 | 0.02 | 0.05 | 0.03 | 0.12 | 0.04 | 0.03 | 0.08 | 0.02 | 0.04 | 0.00 | 0.09 | 0.02 | 0.08 | 0.01 | 0.05 | 0.14 | 0.05 | 0.03 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.06 | 0.07 | 0.26 | 0.12 | 0.01 | 0.03 | 0.03 | 0.02 | 0.00 | 0.03 | 0.15 | 0.13 | 0.57 | 0.00 | 0.00 | 0.04 | 0.00 | 0.13 | 0.03 | 0.03 | 0.02 | 0.06 | 0.00 | 0.01 | 0.04 | 0.03 |
| TAP2 | ENSG00000204267 | 0.01 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.00 | 0.09 | 0.04 | 0.00 | 0.00 | 0.02 | 0.02 | 0.08 | 0.02 | 0.05 | 0.05 | 0.03 | 0.04 | 0.15 | 0.05 | 0.09 | 0.04 | 0.03 | 0.02 | 0.06 | 0.02 | 0.04 | 0.01 | 0.08 | 0.01 | 0.05 | 0.03 | 0.03 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.09 | 0.03 | 0.28 | 0.06 | 0.09 | 0.01 | 0.05 | 0.01 | 0.05 | 0.03 | 0.05 | 0.07 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.17 | 0.01 | 0.01 | 0.01 | 0.01 | 0.11 | 0.00 | 0.11 | 0.01 |
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