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 |
| LALBA | ENSG00000167531 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.05 | 0.03 | 0.00 | 0.00 | 0.00 | 0.04 | 0.06 | 0.02 | 0.05 | 0.02 | 0.01 | 0.04 | 0.05 | 0.04 | 0.05 | 0.04 | 0.02 | 0.00 | 0.02 | 0.02 | 0.00 | 0.04 | 0.01 | 0.01 | 0.09 | 0.01 | 0.19 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.03 | 0.05 | 0.10 | 0.06 | 0.02 | 0.00 | 0.03 | 0.01 | 0.13 | 0.15 | 0.09 | 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 | 0.08 | 0.05 |
| CACNB3 | ENSG00000167535 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.04 | 0.03 | 0.00 | 0.00 | 0.00 | 0.04 | 0.07 | 0.02 | 0.04 | 0.02 | 0.02 | 0.04 | 0.06 | 0.04 | 0.06 | 0.04 | 0.02 | 0.00 | 0.02 | 0.02 | 0.00 | 0.04 | 0.03 | 0.01 | 0.09 | 0.01 | 0.16 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.04 | 0.05 | 0.08 | 0.06 | 0.02 | 0.00 | 0.03 | 0.01 | 0.13 | 0.13 | 0.07 | 0.09 | 0.02 | 0.00 | 0.00 | 0.01 | 0.10 | 0.06 | 0.01 | 0.04 | 0.03 | 0.05 | 0.00 | 0.00 | 0.06 | 0.05 |
| TUBA1A | ENSG00000167552 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.04 | 0.04 | 0.00 | 0.00 | 0.00 | 0.04 | 0.06 | 0.01 | 0.02 | 0.02 | 0.02 | 0.04 | 0.06 | 0.04 | 0.04 | 0.03 | 0.02 | 0.00 | 0.02 | 0.01 | 0.00 | 0.05 | 0.02 | 0.01 | 0.09 | 0.01 | 0.17 | 0.00 | 0.01 | 0.03 | 0.00 | 0.00 | 0.04 | 0.05 | 0.08 | 0.07 | 0.02 | 0.01 | 0.04 | 0.01 | 0.09 | 0.11 | 0.04 | 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 |
| LAIR1 | ENSG00000167613 | 0.01 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.03 | 0.00 | 0.17 | 0.02 | 0.00 | 0.00 | 0.01 | 0.04 | 0.03 | 0.05 | 0.11 | 0.09 | 0.05 | 0.02 | 0.10 | 0.03 | 0.10 | 0.03 | 0.02 | 0.02 | 0.01 | 0.04 | 0.03 | 0.04 | 0.06 | 0.02 | 0.00 | 0.07 | 0.21 | 0.00 | 0.00 | 0.03 | 0.00 | 0.00 | 0.14 | 0.03 | 0.19 | 0.27 | 0.14 | 0.06 | 0.06 | 0.05 | 0.36 | 0.10 | 0.08 | 0.16 | 0.00 | 0.06 | 0.01 | 0.00 | 0.13 | 0.03 | 0.01 | 0.17 | 0.02 | 0.12 | 0.00 | 0.00 | 0.04 | 0.03 |
| LAIR2 | ENSG00000167618 | 0.01 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.03 | 0.00 | 0.17 | 0.03 | 0.00 | 0.00 | 0.01 | 0.04 | 0.04 | 0.05 | 0.11 | 0.09 | 0.05 | 0.02 | 0.09 | 0.03 | 0.11 | 0.03 | 0.02 | 0.02 | 0.01 | 0.04 | 0.03 | 0.04 | 0.06 | 0.02 | 0.00 | 0.07 | 0.21 | 0.00 | 0.00 | 0.03 | 0.00 | 0.00 | 0.15 | 0.03 | 0.16 | 0.27 | 0.12 | 0.06 | 0.06 | 0.05 | 0.36 | 0.10 | 0.07 | 0.16 | 0.00 | 0.06 | 0.01 | 0.00 | 0.13 | 0.03 | 0.00 | 0.17 | 0.03 | 0.12 | 0.00 | 0.00 | 0.04 | 0.03 |
| KIR3DL1 | ENSG00000167633 | 0.01 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.03 | 0.00 | 0.19 | 0.02 | 0.00 | 0.00 | 0.01 | 0.04 | 0.05 | 0.05 | 0.09 | 0.09 | 0.05 | 0.02 | 0.12 | 0.03 | 0.11 | 0.03 | 0.02 | 0.02 | 0.01 | 0.04 | 0.03 | 0.04 | 0.06 | 0.02 | 0.02 | 0.07 | 0.21 | 0.00 | 0.00 | 0.03 | 0.00 | 0.00 | 0.15 | 0.03 | 0.17 | 0.26 | 0.12 | 0.06 | 0.06 | 0.05 | 0.25 | 0.10 | 0.07 | 0.18 | 0.00 | 0.06 | 0.01 | 0.00 | 0.13 | 0.03 | 0.01 | 0.18 | 0.02 | 0.12 | 0.00 | 0.00 | 0.04 | 0.04 |
| SPINT2 | ENSG00000167642 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.02 | 0.02 | 0.01 | 0.34 | 0.01 | 0.00 | 0.00 | 0.05 | 0.02 | 0.21 | 0.03 | 0.57 | 0.03 | 0.07 | 0.01 | 0.17 | 0.03 | 0.10 | 0.03 | 0.04 | 0.01 | 0.01 | 0.01 | 0.19 | 0.00 | 0.03 | 0.01 | 0.12 | 0.03 | 0.06 | 0.03 | 0.01 | 0.02 | 0.00 | 0.00 | 0.17 | 0.02 | 0.71 | 0.11 | 0.29 | 0.03 | 0.18 | 0.03 | 1.14 | 0.09 | 0.23 | 0.09 | 0.00 | 0.04 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.04 | 0.04 | 0.03 | 0.00 | 0.00 | 0.05 | 0.01 |
| PSCA | ENSG00000167653 | 0.02 | 0.00 | 0.02 | 0.00 | 0.06 | 0.00 | 0.04 | 0.02 | 0.20 | 0.02 | 0.02 | 0.00 | 0.10 | 0.04 | 0.26 | 0.01 | 0.36 | 0.02 | 0.29 | 0.00 | 0.41 | 0.02 | 0.22 | 0.02 | 0.15 | 0.03 | 0.24 | 0.03 | 0.15 | 0.01 | 0.35 | 0.02 | 0.25 | 0.01 | 0.04 | 0.00 | 0.01 | 0.03 | 0.00 | 0.01 | 0.42 | 0.05 | 1.46 | 0.05 | 0.21 | 0.01 | 0.10 | 0.02 | 0.14 | 0.03 | 0.21 | 0.06 | 0.05 | 0.03 | 0.02 | 0.00 | 0.26 | 0.01 | 0.17 | 0.03 | 0.04 | 0.03 | 0.50 | 0.00 | 0.24 | 0.02 |
| LY6D | ENSG00000167656 | 0.02 | 0.00 | 0.02 | 0.00 | 0.06 | 0.00 | 0.04 | 0.02 | 0.20 | 0.02 | 0.02 | 0.00 | 0.10 | 0.04 | 0.26 | 0.01 | 0.36 | 0.02 | 0.29 | 0.00 | 0.41 | 0.02 | 0.21 | 0.02 | 0.15 | 0.03 | 0.24 | 0.03 | 0.15 | 0.01 | 0.35 | 0.02 | 0.25 | 0.01 | 0.04 | 0.00 | 0.01 | 0.03 | 0.00 | 0.01 | 0.42 | 0.05 | 1.45 | 0.05 | 0.21 | 0.01 | 0.11 | 0.02 | 0.14 | 0.03 | 0.19 | 0.06 | 0.05 | 0.03 | 0.02 | 0.00 | 0.26 | 0.01 | 0.17 | 0.03 | 0.03 | 0.03 | 0.50 | 0.00 | 0.24 | 0.02 |
| DAPK3 | ENSG00000167657 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.04 | 0.01 | 0.03 | 0.02 | 0.13 | 0.02 | 0.00 | 0.01 | 0.10 | 0.01 | 0.08 | 0.02 | 0.12 | 0.03 | 0.11 | 0.05 | 0.11 | 0.00 | 0.10 | 0.01 | 0.04 | 0.01 | 0.10 | 0.00 | 0.06 | 0.03 | 0.14 | 0.00 | 0.03 | 0.04 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.04 | 0.11 | 0.03 | 0.86 | 0.04 | 0.19 | 0.01 | 0.28 | 0.04 | 0.74 | 0.17 | 0.07 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.03 | 0.01 | 0.02 | 0.04 | 0.02 | 0.00 | 0.05 | 0.05 | 0.05 |
| HDGFRP2 | ENSG00000167674 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.04 | 0.01 | 0.04 | 0.03 | 0.12 | 0.00 | 0.01 | 0.01 | 0.10 | 0.01 | 0.08 | 0.03 | 0.12 | 0.02 | 0.11 | 0.06 | 0.13 | 0.01 | 0.10 | 0.01 | 0.05 | 0.01 | 0.09 | 0.00 | 0.06 | 0.05 | 0.13 | 0.00 | 0.03 | 0.04 | 0.04 | 0.01 | 0.00 | 0.00 | 0.01 | 0.05 | 0.11 | 0.03 | 0.79 | 0.03 | 0.18 | 0.01 | 0.27 | 0.05 | 0.71 | 0.14 | 0.07 | 0.00 | 0.00 | 0.04 | 0.00 | 0.00 | 0.06 | 0.01 | 0.01 | 0.05 | 0.01 | 0.00 | 0.05 | 0.04 | 0.04 |
| SEMA6B | ENSG00000167680 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.04 | 0.01 | 0.04 | 0.03 | 0.12 | 0.00 | 0.01 | 0.01 | 0.10 | 0.01 | 0.08 | 0.04 | 0.12 | 0.03 | 0.11 | 0.04 | 0.13 | 0.00 | 0.10 | 0.01 | 0.05 | 0.06 | 0.09 | 0.00 | 0.06 | 0.03 | 0.13 | 0.00 | 0.03 | 0.04 | 0.04 | 0.01 | 0.00 | 0.00 | 0.01 | 0.05 | 0.11 | 0.04 | 0.79 | 0.03 | 0.18 | 0.01 | 0.27 | 0.08 | 0.71 | 0.15 | 0.07 | 0.00 | 0.00 | 0.04 | 0.00 | 0.00 | 0.06 | 0.01 | 0.01 | 0.04 | 0.01 | 0.00 | 0.05 | 0.04 | 0.04 |
| SLC43A2 | ENSG00000167703 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.06 | 0.05 | 0.05 | 0.00 | 0.00 | 0.01 | 0.03 | 0.01 | 0.07 | 0.03 | 0.03 | 0.02 | 0.04 | 0.05 | 0.06 | 0.04 | 0.03 | 0.04 | 0.02 | 0.01 | 0.00 | 0.00 | 0.03 | 0.04 | 0.14 | 0.01 | 0.03 | 0.05 | 0.05 | 0.01 | 0.04 | 0.00 | 0.00 | 0.03 | 0.06 | 0.18 | 0.10 | 0.02 | 0.04 | 0.09 | 0.05 | 0.19 | 0.12 | 0.18 | 0.22 | 0.01 | 0.02 | 0.00 | 0.02 | 0.00 | 0.06 | 0.01 | 0.00 | 0.01 | 0.04 | 0.00 | 0.00 | 0.02 | 0.06 |
| CYB5D2 | ENSG00000167740 | 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 | 0.06 | 0.02 | 0.04 | 0.02 | 0.04 | 0.05 | 0.08 | 0.03 | 0.02 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.12 | 0.02 | 0.03 | 0.02 | 0.05 | 0.00 | 0.03 | 0.00 | 0.00 | 0.03 | 0.05 | 0.11 | 0.08 | 0.01 | 0.03 | 0.05 | 0.04 | 0.06 | 0.11 | 0.15 | 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 | 0.04 | 0.03 |
| KLK5 | ENSG00000167754 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.02 | 0.00 | 0.13 | 0.04 | 0.00 | 0.00 | 0.02 | 0.06 | 0.02 | 0.08 | 0.07 | 0.10 | 0.03 | 0.02 | 0.07 | 0.03 | 0.09 | 0.03 | 0.02 | 0.03 | 0.02 | 0.04 | 0.04 | 0.04 | 0.05 | 0.03 | 0.00 | 0.07 | 0.23 | 0.02 | 0.00 | 0.03 | 0.00 | 0.00 | 0.11 | 0.03 | 0.10 | 0.30 | 0.06 | 0.07 | 0.04 | 0.05 | 0.24 | 0.13 | 0.03 | 0.17 | 0.00 | 0.04 | 0.01 | 0.00 | 0.13 | 0.03 | 0.01 | 0.16 | 0.01 | 0.14 | 0.00 | 0.00 | 0.03 | 0.03 |
| KLK6 | ENSG00000167755 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.02 | 0.00 | 0.13 | 0.04 | 0.00 | 0.00 | 0.00 | 0.06 | 0.02 | 0.08 | 0.07 | 0.10 | 0.03 | 0.02 | 0.07 | 0.03 | 0.09 | 0.03 | 0.02 | 0.02 | 0.02 | 0.04 | 0.04 | 0.04 | 0.05 | 0.03 | 0.00 | 0.07 | 0.23 | 0.02 | 0.00 | 0.03 | 0.00 | 0.00 | 0.11 | 0.04 | 0.10 | 0.30 | 0.06 | 0.07 | 0.04 | 0.05 | 0.24 | 0.13 | 0.03 | 0.17 | 0.00 | 0.04 | 0.01 | 0.00 | 0.13 | 0.03 | 0.01 | 0.16 | 0.01 | 0.14 | 0.00 | 0.00 | 0.03 | 0.03 |
| KLK13 | ENSG00000167759 | 0.01 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.02 | 0.00 | 0.13 | 0.04 | 0.00 | 0.00 | 0.00 | 0.06 | 0.02 | 0.08 | 0.07 | 0.10 | 0.03 | 0.02 | 0.07 | 0.03 | 0.09 | 0.03 | 0.02 | 0.02 | 0.02 | 0.04 | 0.04 | 0.04 | 0.04 | 0.03 | 0.00 | 0.07 | 0.23 | 0.02 | 0.00 | 0.03 | 0.00 | 0.00 | 0.13 | 0.04 | 0.10 | 0.31 | 0.07 | 0.07 | 0.04 | 0.06 | 0.22 | 0.13 | 0.02 | 0.18 | 0.00 | 0.04 | 0.01 | 0.00 | 0.13 | 0.03 | 0.01 | 0.16 | 0.01 | 0.15 | 0.00 | 0.00 | 0.03 | 0.03 |
| ANGPTL4 | ENSG00000167772 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.02 | 0.00 | 0.02 | 0.06 | 0.09 | 0.00 | 0.01 | 0.04 | 0.07 | 0.01 | 0.06 | 0.06 | 0.08 | 0.04 | 0.08 | 0.03 | 0.10 | 0.02 | 0.08 | 0.01 | 0.03 | 0.00 | 0.06 | 0.02 | 0.04 | 0.01 | 0.12 | 0.00 | 0.01 | 0.07 | 0.03 | 0.01 | 0.00 | 0.00 | 0.01 | 0.07 | 0.07 | 0.35 | 0.40 | 0.10 | 0.12 | 0.10 | 0.18 | 0.13 | 0.49 | 0.21 | 0.01 | 0.02 | 0.00 | 0.02 | 0.00 | 0.00 | 0.08 | 0.00 | 0.01 | 0.03 | 0.01 | 0.00 | 0.05 | 0.02 | 0.03 |
| CD320 | ENSG00000167775 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.02 | 0.00 | 0.02 | 0.06 | 0.09 | 0.00 | 0.01 | 0.01 | 0.07 | 0.01 | 0.06 | 0.05 | 0.08 | 0.03 | 0.08 | 0.01 | 0.10 | 0.02 | 0.08 | 0.01 | 0.03 | 0.00 | 0.06 | 0.02 | 0.04 | 0.01 | 0.12 | 0.00 | 0.01 | 0.07 | 0.03 | 0.01 | 0.00 | 0.00 | 0.01 | 0.07 | 0.07 | 0.31 | 0.40 | 0.06 | 0.12 | 0.10 | 0.18 | 0.10 | 0.49 | 0.23 | 0.01 | 0.02 | 0.00 | 0.02 | 0.00 | 0.00 | 0.08 | 0.00 | 0.01 | 0.03 | 0.01 | 0.00 | 0.05 | 0.02 | 0.03 |
| OR8J3 | ENSG00000167822 | 0.01 | 0.00 | 0.00 | 0.01 | 0.08 | 0.00 | 0.01 | 0.03 | 0.13 | 0.04 | 0.00 | 0.01 | 0.04 | 0.03 | 0.04 | 0.03 | 0.08 | 0.03 | 0.11 | 0.01 | 0.16 | 0.05 | 0.01 | 0.04 | 0.02 | 0.01 | 0.01 | 0.02 | 0.00 | 0.01 | 0.02 | 0.02 | 0.05 | 0.07 | 0.07 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.09 | 0.07 | 0.12 | 0.06 | 0.04 | 0.02 | 0.04 | 0.03 | 0.34 | 0.03 | 0.10 | 0.05 | 0.01 | 0.03 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.02 | 0.01 | 0.02 | 0.00 | 0.02 | 0.05 | 0.04 |
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