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 |
| BTNL9 | ENSG00000165810 | 0.33 | 0.00 | 0.06 | 0.01 | 0.00 | 0.04 | 0.03 | 0.01 | 0.02 | 0.10 | 0.00 | 0.01 | 0.03 | 0.05 | 0.09 | 0.03 | 0.04 | 0.06 | 0.04 | 0.06 | 0.18 | 0.02 | 0.03 | 0.05 | 0.03 | 0.01 | 0.04 | 0.04 | 0.03 | 0.01 | 0.14 | 0.05 | 0.05 | 0.01 | 0.38 | 0.03 | 0.01 | 0.03 | 0.01 | 0.00 | 0.10 | 0.05 | 0.23 | 0.15 | 0.04 | 0.04 | 0.07 | 0.03 | 0.21 | 0.02 | 0.23 | 0.11 | 0.00 | 0.01 | 0.00 | 0.02 | 0.02 | 0.00 | 0.01 | 0.06 | 0.03 | 0.04 | 0.04 | 0.02 | 0.08 | 0.07 |
| PRAP1 | ENSG00000165828 | 0.01 | 0.02 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.06 | 0.06 | 0.10 | 0.02 | 0.02 | 0.02 | 0.14 | 0.05 | 0.06 | 0.07 | 0.07 | 0.03 | 0.04 | 0.05 | 0.10 | 0.09 | 0.08 | 0.02 | 0.06 | 0.02 | 0.06 | 0.01 | 0.01 | 0.02 | 0.10 | 0.14 | 0.17 | 0.09 | 0.10 | 0.00 | 0.02 | 0.00 | 0.00 | 0.07 | 0.12 | 0.25 | 0.23 | 0.03 | 0.06 | 0.06 | 0.06 | 0.08 | 0.04 | 0.06 | 0.18 | 0.03 | 0.17 | 0.02 | 0.01 | 0.03 | 0.03 | 0.00 | 0.14 | 0.00 | 0.17 | 0.00 | 0.00 | 0.01 | 0.11 |
| SLC39A13 | ENSG00000165915 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.00 | 0.00 | 0.08 | 0.03 | 0.06 | 0.00 | 0.00 | 0.00 | 0.01 | 0.04 | 0.02 | 0.11 | 0.04 | 0.06 | 0.01 | 0.08 | 0.04 | 0.06 | 0.01 | 0.00 | 0.01 | 0.01 | 0.00 | 0.03 | 0.01 | 0.03 | 0.00 | 0.00 | 0.07 | 0.12 | 0.02 | 0.00 | 0.03 | 0.00 | 0.00 | 0.07 | 0.03 | 0.12 | 0.07 | 0.07 | 0.03 | 0.06 | 0.02 | 0.11 | 0.15 | 0.09 | 0.07 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.01 | 0.04 | 0.00 | 0.02 | 0.01 | 0.04 |
| AGBL2 | ENSG00000165923 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.00 | 0.00 | 0.08 | 0.02 | 0.05 | 0.00 | 0.01 | 0.00 | 0.01 | 0.04 | 0.02 | 0.08 | 0.04 | 0.06 | 0.01 | 0.07 | 0.04 | 0.04 | 0.01 | 0.01 | 0.01 | 0.02 | 0.00 | 0.01 | 0.02 | 0.03 | 0.00 | 0.00 | 0.07 | 0.08 | 0.02 | 0.00 | 0.03 | 0.00 | 0.00 | 0.07 | 0.03 | 0.11 | 0.07 | 0.06 | 0.03 | 0.04 | 0.03 | 0.10 | 0.07 | 0.08 | 0.07 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.01 | 0.04 | 0.00 | 0.02 | 0.01 | 0.05 |
| SLC6A5 | ENSG00000165970 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.04 | 0.00 | 0.00 | 0.03 | 0.07 | 0.00 | 0.00 | 0.00 | 0.01 | 0.03 | 0.03 | 0.06 | 0.06 | 0.01 | 0.04 | 0.07 | 0.04 | 0.02 | 0.02 | 0.02 | 0.00 | 0.02 | 0.01 | 0.00 | 0.02 | 0.03 | 0.02 | 0.00 | 0.01 | 0.02 | 0.02 | 0.04 | 0.04 | 0.00 | 0.00 | 0.07 | 0.04 | 0.06 | 0.19 | 0.02 | 0.05 | 0.02 | 0.03 | 0.01 | 0.04 | 0.04 | 0.09 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.01 | 0.02 | 0.00 | 0.00 | 0.03 | 0.01 |
| LIPC | ENSG00000166035 | 0.00 | 0.00 | 0.00 | 0.01 | 0.14 | 0.02 | 0.01 | 0.04 | 0.06 | 0.05 | 0.00 | 0.00 | 0.08 | 0.07 | 0.02 | 0.04 | 0.04 | 0.04 | 0.01 | 0.03 | 0.03 | 0.03 | 0.03 | 0.05 | 0.01 | 0.04 | 0.00 | 0.07 | 0.01 | 0.02 | 0.05 | 0.02 | 0.00 | 0.01 | 0.04 | 0.05 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.07 | 0.06 | 0.15 | 0.03 | 0.06 | 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 |
| JAM3 | ENSG00000166086 | 0.00 | 0.01 | 0.00 | 0.04 | 0.02 | 0.03 | 0.02 | 0.02 | 0.03 | 0.12 | 0.00 | 0.00 | 0.11 | 0.03 | 0.06 | 0.11 | 0.08 | 0.14 | 0.04 | 0.15 | 0.10 | 0.18 | 0.04 | 0.09 | 0.02 | 0.01 | 0.01 | 0.02 | 0.03 | 0.02 | 0.02 | 0.10 | 0.00 | 0.31 | 0.02 | 0.06 | 0.00 | 0.06 | 0.00 | 0.00 | 0.04 | 0.22 | 0.28 | 0.21 | 0.04 | 0.31 | 0.04 | 0.09 | 0.08 | 0.17 | 0.04 | 0.29 | 0.00 | 0.28 | 0.04 | 0.00 | 0.13 | 0.00 | 0.06 | 0.04 | 0.03 | 0.02 | 0.05 | 0.05 | 0.01 | 0.25 |
| IL25 | ENSG00000166090 | 0.00 | 0.00 | 0.03 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.14 | 0.06 | 0.01 | 0.00 | 0.00 | 0.02 | 0.18 | 0.03 | 0.16 | 0.07 | 0.06 | 0.07 | 0.12 | 0.05 | 0.05 | 0.04 | 0.02 | 0.02 | 0.01 | 0.07 | 0.01 | 0.03 | 0.08 | 0.00 | 0.00 | 0.02 | 0.28 | 0.03 | 0.00 | 0.02 | 0.00 | 0.00 | 0.12 | 0.03 | 0.26 | 0.12 | 0.08 | 0.02 | 0.05 | 0.03 | 0.06 | 0.07 | 0.23 | 0.03 | 0.01 | 0.03 | 0.00 | 0.01 | 0.00 | 0.00 | 0.03 | 0.03 | 0.02 | 0.09 | 0.00 | 0.00 | 0.03 | 0.03 |
| ADAMTS15 | ENSG00000166106 | 0.00 | 0.01 | 0.00 | 0.05 | 0.00 | 0.05 | 0.03 | 0.04 | 0.03 | 0.11 | 0.00 | 0.00 | 0.14 | 0.06 | 0.06 | 0.09 | 0.05 | 0.13 | 0.04 | 0.14 | 0.09 | 0.14 | 0.06 | 0.07 | 0.01 | 0.01 | 0.01 | 0.02 | 0.02 | 0.02 | 0.03 | 0.09 | 0.00 | 0.23 | 0.02 | 0.06 | 0.00 | 0.05 | 0.00 | 0.00 | 0.04 | 0.20 | 0.26 | 0.18 | 0.04 | 0.31 | 0.06 | 0.07 | 0.16 | 0.19 | 0.04 | 0.24 | 0.00 | 0.28 | 0.04 | 0.00 | 0.13 | 0.00 | 0.05 | 0.01 | 0.01 | 0.01 | 0.00 | 0.07 | 0.01 | 0.26 |
| SVOP | ENSG00000166111 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |
| AVPR1A | ENSG00000166148 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.07 | 0.03 | 0.00 | 0.00 | 0.02 | 0.05 | 0.17 | 0.01 | 0.09 | 0.02 | 0.10 | 0.01 | 0.12 | 0.02 | 0.13 | 0.01 | 0.01 | 0.00 | 0.02 | 0.03 | 0.02 | 0.02 | 0.03 | 0.01 | 0.25 | 0.01 | 0.16 | 0.10 | 0.05 | 0.00 | 0.01 | 0.00 | 0.12 | 0.03 | 0.17 | 0.05 | 0.03 | 0.01 | 0.02 | 0.01 | 0.19 | 0.04 | 0.24 | 0.05 | 0.02 | 0.00 | 0.00 | 0.01 | 0.12 | 0.00 | 0.02 | 0.02 | 0.09 | 0.05 | 0.00 | 0.00 | 0.04 | 0.02 |
| OPN1MW2 | ENSG00000166160 | 0.03 | 0.01 | 0.02 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.12 | 0.04 | 0.06 | 0.00 | 0.06 | 0.01 | 0.23 | 0.01 | 0.19 | 0.03 | 0.15 | 0.00 | 0.23 | 0.02 | 0.17 | 0.02 | 0.05 | 0.00 | 0.10 | 0.01 | 0.06 | 0.00 | 0.13 | 0.03 | 0.10 | 0.01 | 0.17 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.10 | 0.03 | 0.46 | 0.10 | 0.23 | 0.02 | 0.11 | 0.03 | 0.09 | 0.07 | 0.23 | 0.08 | 0.01 | 0.02 | 0.00 | 0.00 | 0.15 | 0.07 | 0.02 | 0.03 | 0.04 | 0.01 | 0.05 | 0.00 | 0.07 | 0.01 |
| SENP8 | ENSG00000166192 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.02 | 0.01 | 0.02 | 0.05 | 0.02 | 0.00 | 0.00 | 0.09 | 0.02 | 0.04 | 0.02 | 0.06 | 0.02 | 0.04 | 0.02 | 0.07 | 0.04 | 0.08 | 0.03 | 0.02 | 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 | 0.10 | 0.10 | 0.01 | 0.06 | 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 |
| SCN3B | ENSG00000166257 | 0.00 | 0.01 | 0.00 | 0.05 | 0.02 | 0.02 | 0.02 | 0.06 | 0.03 | 0.10 | 0.00 | 0.00 | 0.13 | 0.06 | 0.05 | 0.09 | 0.05 | 0.10 | 0.04 | 0.14 | 0.05 | 0.13 | 0.05 | 0.08 | 0.01 | 0.01 | 0.01 | 0.03 | 0.01 | 0.02 | 0.00 | 0.09 | 0.00 | 0.19 | 0.00 | 0.08 | 0.00 | 0.05 | 0.00 | 0.00 | 0.04 | 0.22 | 0.18 | 0.17 | 0.04 | 0.31 | 0.04 | 0.07 | 0.05 | 0.17 | 0.02 | 0.24 | 0.00 | 0.23 | 0.03 | 0.00 | 0.13 | 0.02 | 0.06 | 0.01 | 0.01 | 0.01 | 0.00 | 0.07 | 0.00 | 0.25 |
| C2 | ENSG00000166278 | 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 |
| ILK | ENSG00000166333 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.03 | 0.01 | 0.01 | 0.00 | 0.09 | 0.00 | 0.00 | 0.02 | 0.08 | 0.01 | 0.06 | 0.02 | 0.13 | 0.01 | 0.06 | 0.06 | 0.09 | 0.01 | 0.04 | 0.01 | 0.01 | 0.01 | 0.02 | 0.00 | 0.05 | 0.04 | 0.02 | 0.03 | 0.01 | 0.04 | 0.07 | 0.02 | 0.07 | 0.00 | 0.00 | 0.03 | 0.10 | 0.01 | 0.41 | 0.01 | 0.05 | 0.02 | 0.06 | 0.03 | 0.09 | 0.04 | 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 | 0.02 | 0.03 |
| TPP1 | ENSG00000166340 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.03 | 0.01 | 0.01 | 0.00 | 0.09 | 0.00 | 0.00 | 0.02 | 0.08 | 0.01 | 0.06 | 0.02 | 0.13 | 0.01 | 0.06 | 0.06 | 0.09 | 0.01 | 0.04 | 0.01 | 0.01 | 0.01 | 0.02 | 0.00 | 0.05 | 0.04 | 0.02 | 0.03 | 0.01 | 0.04 | 0.07 | 0.02 | 0.07 | 0.00 | 0.00 | 0.03 | 0.10 | 0.01 | 0.41 | 0.01 | 0.05 | 0.02 | 0.06 | 0.03 | 0.09 | 0.04 | 0.13 | 0.02 | 0.00 | 0.00 | 0.00 | 0.05 | 0.00 | 0.01 | 0.08 | 0.01 | 0.05 | 0.00 | 0.00 | 0.02 | 0.03 |
| OR10A5 | ENSG00000166363 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.03 | 0.01 | 0.02 | 0.00 | 0.09 | 0.00 | 0.03 | 0.02 | 0.07 | 0.02 | 0.06 | 0.02 | 0.14 | 0.01 | 0.06 | 0.05 | 0.10 | 0.01 | 0.04 | 0.01 | 0.01 | 0.01 | 0.02 | 0.00 | 0.05 | 0.03 | 0.02 | 0.03 | 0.01 | 0.02 | 0.07 | 0.02 | 0.07 | 0.00 | 0.00 | 0.04 | 0.10 | 0.01 | 0.41 | 0.01 | 0.05 | 0.02 | 0.06 | 0.03 | 0.18 | 0.03 | 0.12 | 0.02 | 0.00 | 0.00 | 0.00 | 0.05 | 0.00 | 0.01 | 0.09 | 0.01 | 0.04 | 0.03 | 0.00 | 0.01 | 0.02 |
| OR2D2 | ENSG00000166368 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.03 | 0.01 | 0.02 | 0.00 | 0.09 | 0.00 | 0.00 | 0.02 | 0.07 | 0.02 | 0.06 | 0.02 | 0.13 | 0.01 | 0.06 | 0.05 | 0.12 | 0.02 | 0.04 | 0.01 | 0.01 | 0.01 | 0.03 | 0.00 | 0.05 | 0.03 | 0.02 | 0.03 | 0.01 | 0.01 | 0.07 | 0.02 | 0.07 | 0.00 | 0.00 | 0.03 | 0.10 | 0.01 | 0.41 | 0.01 | 0.05 | 0.02 | 0.07 | 0.03 | 0.18 | 0.03 | 0.13 | 0.02 | 0.00 | 0.00 | 0.00 | 0.05 | 0.00 | 0.01 | 0.09 | 0.01 | 0.04 | 0.03 | 0.00 | 0.01 | 0.03 |
| SERPINB8 | ENSG00000166401 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.10 | 0.01 | 0.09 | 0.00 | 0.00 | 0.00 | 0.02 | 0.03 | 0.09 | 0.04 | 0.06 | 0.02 | 0.15 | 0.06 | 0.19 | 0.02 | 0.16 | 0.00 | 0.12 | 0.01 | 0.12 | 0.01 | 0.08 | 0.02 | 0.06 | 0.00 | 0.10 | 0.01 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.08 | 0.05 | 0.07 | 0.34 | 0.02 | 0.03 | 0.00 | 0.07 | 0.01 | 0.11 | 0.09 | 0.07 | 0.00 | 0.07 | 0.00 | 0.00 | 0.10 | 0.00 | 0.01 | 0.02 | 0.00 | 0.03 | 0.00 | 0.01 | 0.03 | 0.01 |
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