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 |
| NRG3 | ENSG00000185737 | 0.01 | 0.01 | 0.00 | 0.00 | 0.03 | 0.05 | 0.01 | 0.11 | 0.08 | 0.06 | 0.00 | 0.01 | 0.04 | 0.14 | 0.02 | 0.03 | 0.04 | 0.06 | 0.04 | 0.04 | 0.06 | 0.07 | 0.09 | 0.07 | 0.05 | 0.06 | 0.03 | 0.03 | 0.06 | 0.02 | 0.01 | 0.05 | 0.25 | 0.05 | 0.02 | 0.03 | 0.01 | 0.01 | 0.00 | 0.01 | 0.12 | 0.06 | 0.20 | 0.20 | 0.03 | 0.03 | 0.07 | 0.06 | 0.20 | 0.10 | 0.01 | 0.07 | 0.01 | 0.06 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.03 | 0.00 | 0.03 | 0.01 | 0.00 | 0.01 | 0.05 |
| TKT | ENSG00000163931 | 0.00 | 0.16 | 0.00 | 0.02 | 0.00 | 0.02 | 0.00 | 0.03 | 0.04 | 0.15 | 0.00 | 0.03 | 0.00 | 0.55 | 0.01 | 0.06 | 0.00 | 0.11 | 0.00 | 0.06 | 0.05 | 0.12 | 0.01 | 0.11 | 0.00 | 0.06 | 0.02 | 0.07 | 0.00 | 0.04 | 0.03 | 0.06 | 0.00 | 0.20 | 0.15 | 0.01 | 0.00 | 0.04 | 0.00 | 0.00 | 0.01 | 0.16 | 0.11 | 0.21 | 0.00 | 0.07 | 0.06 | 0.07 | 0.04 | 0.32 | 0.03 | 0.15 | 0.05 | 0.01 | 0.00 | 0.01 | 0.00 | 0.06 | 0.01 | 0.05 | 0.00 | 0.05 | 0.00 | 0.06 | 0.02 | 0.04 |
| BAP1 | ENSG00000163930 | 0.00 | 0.18 | 0.00 | 0.03 | 0.00 | 0.02 | 0.00 | 0.03 | 0.04 | 0.17 | 0.00 | 0.01 | 0.00 | 0.77 | 0.01 | 0.05 | 0.00 | 0.11 | 0.00 | 0.06 | 0.02 | 0.13 | 0.01 | 0.11 | 0.00 | 0.06 | 0.02 | 0.07 | 0.00 | 0.05 | 0.04 | 0.06 | 0.00 | 0.20 | 0.06 | 0.01 | 0.00 | 0.04 | 0.00 | 0.00 | 0.01 | 0.17 | 0.09 | 0.23 | 0.00 | 0.10 | 0.09 | 0.06 | 0.05 | 0.27 | 0.04 | 0.15 | 0.05 | 0.01 | 0.00 | 0.01 | 0.00 | 0.06 | 0.01 | 0.06 | 0.03 | 0.04 | 0.00 | 0.03 | 0.02 | 0.05 |
| BIRC7 | ENSG00000101197 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.04 | 0.01 | 0.07 | 0.04 | 0.00 | 0.00 | 0.03 | 0.00 | 0.28 | 0.01 | 0.06 | 0.04 | 0.02 | 0.01 | 0.16 | 0.01 | 0.15 | 0.00 | 0.08 | 0.00 | 0.11 | 0.01 | 0.03 | 0.00 | 0.11 | 0.00 | 0.00 | 0.01 | 0.05 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.33 | 0.02 | 0.48 | 0.04 | 0.04 | 0.03 | 0.13 | 0.01 | 0.28 | 0.00 | 0.18 | 0.08 | 0.03 | 0.03 | 0.03 | 0.00 | 0.04 | 0.00 | 0.02 | 0.01 | 0.01 | 0.02 | 0.00 | 0.00 | 0.15 | 0.00 |
| COL24A1 | ENSG00000171502 | 0.00 | 0.00 | 0.01 | 0.02 | 0.00 | 0.00 | 0.01 | 0.06 | 0.05 | 0.07 | 0.00 | 0.00 | 0.00 | 0.30 | 0.04 | 0.08 | 0.04 | 0.06 | 0.01 | 0.06 | 0.01 | 0.07 | 0.01 | 0.07 | 0.00 | 0.07 | 0.01 | 0.10 | 0.00 | 0.01 | 0.01 | 0.03 | 0.06 | 0.13 | 0.04 | 0.07 | 0.00 | 0.23 | 0.00 | 0.00 | 0.05 | 0.10 | 0.11 | 0.19 | 0.01 | 0.04 | 0.01 | 0.03 | 0.07 | 0.05 | 0.12 | 0.06 | 0.03 | 0.05 | 0.01 | 0.01 | 0.06 | 0.03 | 0.01 | 0.01 | 0.01 | 0.04 | 0.03 | 0.03 | 0.03 | 0.11 |
| DPP10 | ENSG00000175497 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.09 | 0.06 | 0.02 | 0.00 | 0.01 | 0.00 | 0.02 | 0.05 | 0.01 | 0.11 | 0.02 | 0.09 | 0.01 | 0.22 | 0.03 | 0.07 | 0.02 | 0.00 | 0.01 | 0.00 | 0.01 | 0.01 | 0.02 | 0.01 | 0.04 | 0.00 | 0.01 | 0.07 | 0.04 | 0.01 | 0.00 | 0.00 | 0.00 | 0.05 | 0.03 | 0.15 | 0.12 | 0.04 | 0.01 | 0.08 | 0.01 | 0.09 | 0.00 | 0.11 | 0.02 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.08 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 |
| ZMYND11 | ENSG00000015171 | 0.01 | 0.02 | 0.03 | 0.02 | 0.00 | 0.04 | 0.01 | 0.03 | 0.24 | 0.02 | 0.00 | 0.00 | 0.02 | 0.17 | 0.06 | 0.09 | 0.03 | 0.13 | 0.03 | 0.06 | 0.07 | 0.12 | 0.06 | 0.06 | 0.02 | 0.04 | 0.02 | 0.03 | 0.01 | 0.05 | 0.03 | 0.03 | 0.00 | 0.05 | 0.00 | 0.03 | 0.01 | 0.01 | 0.00 | 0.00 | 0.16 | 0.03 | 0.34 | 0.18 | 0.04 | 0.03 | 0.07 | 0.03 | 0.32 | 0.00 | 0.09 | 0.35 | 0.01 | 0.07 | 0.01 | 0.02 | 0.07 | 0.09 | 0.08 | 0.02 | 0.02 | 0.06 | 0.00 | 0.02 | 0.03 | 0.10 |
| TOP1 | ENSG00000198900 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.09 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.03 | 0.04 | 0.09 | 0.01 | 0.01 | 0.02 | 0.04 | 0.01 | 0.10 | 0.01 | 0.08 | 0.00 | 0.14 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.00 | 0.04 | 0.08 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.12 | 0.03 | 0.05 | 0.10 | 0.02 | 0.02 | 0.04 | 0.02 | 0.20 | 0.04 | 0.17 | 0.04 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.02 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.04 | 0.00 |
| NT5E | ENSG00000135318 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.37 | 0.02 | 0.07 | 0.00 | 0.00 | 0.01 | 0.03 | 0.02 | 0.06 | 0.10 | 0.03 | 0.03 | 0.03 | 0.10 | 0.06 | 0.02 | 0.08 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.03 | 0.03 | 0.05 | 0.00 | 0.20 | 0.09 | 0.05 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.10 | 0.12 | 0.11 | 0.01 | 0.01 | 0.02 | 0.02 | 0.03 | 0.06 | 0.05 | 0.12 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.22 | 0.01 | 0.01 | 0.00 | 0.03 | 0.04 | 0.03 | 0.02 | 0.04 |
| BMP2K | ENSG00000138756 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.03 | 0.01 | 0.07 | 0.02 | 0.00 | 0.00 | 0.00 | 0.08 | 0.06 | 0.03 | 0.12 | 0.04 | 0.05 | 0.03 | 0.07 | 0.07 | 0.03 | 0.05 | 0.01 | 0.01 | 0.03 | 0.01 | 0.01 | 0.00 | 0.02 | 0.09 | 0.00 | 0.08 | 0.11 | 0.02 | 0.02 | 0.02 | 0.00 | 0.00 | 0.07 | 0.03 | 0.11 | 0.20 | 0.06 | 0.03 | 0.04 | 0.02 | 0.06 | 0.05 | 0.05 | 0.05 | 0.03 | 0.02 | 0.00 | 0.01 | 0.00 | 0.05 | 0.01 | 0.02 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.02 |
| TYMP | ENSG00000025708 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.03 | 0.01 | 0.03 | 0.01 | 0.12 | 0.00 | 0.03 | 0.00 | 0.06 | 0.02 | 0.12 | 0.06 | 0.09 | 0.02 | 0.04 | 0.03 | 0.03 | 0.03 | 0.07 | 0.00 | 0.04 | 0.01 | 0.09 | 0.01 | 0.10 | 0.07 | 0.07 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.06 | 0.00 | 0.01 | 0.06 | 0.06 | 0.02 | 0.64 | 0.03 | 0.07 | 0.03 | 0.15 | 0.06 | 0.27 | 0.06 | 0.15 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.09 | 0.00 | 0.05 | 0.00 | 0.10 | 0.00 | 0.00 | 0.12 | 0.05 |
| CPAMD8 | ENSG00000160111 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.01 | 0.05 | 0.00 | 0.03 | 0.05 | 0.01 | 0.01 | 0.02 | 0.08 | 0.03 | 0.04 | 0.02 | 0.13 | 0.01 | 0.03 | 0.01 | 0.02 | 0.00 | 0.01 | 0.03 | 0.01 | 0.01 | 0.05 | 0.03 | 0.04 | 0.03 | 0.18 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.10 | 0.02 | 0.71 | 0.02 | 0.02 | 0.01 | 0.25 | 0.01 | 0.32 | 0.05 | 0.11 | 0.02 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.01 | 0.01 | 0.02 | 0.00 | 0.02 | 0.00 |
| PTPN13 | ENSG00000163629 | 0.01 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.03 | 0.03 | 0.17 | 0.12 | 0.00 | 0.00 | 0.00 | 0.08 | 0.02 | 0.04 | 0.07 | 0.06 | 0.04 | 0.09 | 0.05 | 0.12 | 0.03 | 0.07 | 0.01 | 0.02 | 0.00 | 0.03 | 0.00 | 0.01 | 0.02 | 0.13 | 0.00 | 0.03 | 0.09 | 0.02 | 0.02 | 0.02 | 0.00 | 0.00 | 0.04 | 0.04 | 0.05 | 0.24 | 0.08 | 0.10 | 0.03 | 0.03 | 0.02 | 0.19 | 0.08 | 0.08 | 0.00 | 0.03 | 0.00 | 0.01 | 0.04 | 0.08 | 0.00 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.05 |
| AKT3 | ENSG00000117020 | 0.01 | 0.03 | 0.01 | 0.01 | 0.00 | 0.01 | 0.04 | 0.04 | 0.11 | 0.04 | 0.02 | 0.00 | 0.10 | 0.04 | 0.13 | 0.01 | 0.15 | 0.02 | 0.10 | 0.01 | 0.25 | 0.06 | 0.12 | 0.02 | 0.04 | 0.03 | 0.08 | 0.02 | 0.02 | 0.01 | 0.19 | 0.02 | 0.23 | 0.02 | 0.06 | 0.03 | 0.00 | 0.05 | 0.00 | 0.00 | 0.29 | 0.02 | 0.49 | 0.12 | 0.12 | 0.02 | 0.11 | 0.02 | 0.32 | 0.00 | 0.08 | 0.22 | 0.06 | 0.02 | 0.01 | 0.00 | 0.07 | 0.21 | 0.03 | 0.03 | 0.15 | 0.02 | 0.08 | 0.04 | 0.26 | 0.02 |
| CD101 | ENSG00000134256 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.02 | 0.03 | 0.11 | 0.04 | 0.00 | 0.00 | 0.00 | 0.26 | 0.02 | 0.14 | 0.04 | 0.19 | 0.03 | 0.16 | 0.14 | 0.14 | 0.03 | 0.08 | 0.01 | 0.06 | 0.02 | 0.08 | 0.11 | 0.01 | 0.01 | 0.04 | 0.00 | 0.10 | 0.05 | 0.05 | 0.04 | 0.26 | 0.00 | 0.00 | 0.07 | 0.07 | 0.20 | 0.10 | 0.01 | 0.08 | 0.05 | 0.03 | 0.05 | 0.06 | 0.07 | 0.11 | 0.07 | 0.02 | 0.00 | 0.01 | 0.03 | 0.15 | 0.00 | 0.01 | 0.01 | 0.03 | 0.00 | 0.05 | 0.10 | 0.09 |
| F10 | ENSG00000126218 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.04 | 0.22 | 0.01 | 0.00 | 0.01 | 0.01 | 0.02 | 0.12 | 0.07 | 0.23 | 0.05 | 0.15 | 0.01 | 0.22 | 0.03 | 0.15 | 0.03 | 0.11 | 0.01 | 0.17 | 0.02 | 0.02 | 0.02 | 0.29 | 0.00 | 0.06 | 0.04 | 0.13 | 0.03 | 0.02 | 0.00 | 0.00 | 0.00 | 0.17 | 0.05 | 0.26 | 0.14 | 0.23 | 0.01 | 0.09 | 0.03 | 0.33 | 0.12 | 0.45 | 0.10 | 0.01 | 0.04 | 0.00 | 0.00 | 0.02 | 0.12 | 0.04 | 0.03 | 0.05 | 0.02 | 0.08 | 0.00 | 0.07 | 0.07 |
| TP73 | ENSG00000078900 | 0.00 | 0.05 | 0.01 | 0.10 | 0.00 | 0.00 | 0.02 | 0.03 | 0.10 | 0.08 | 0.00 | 0.02 | 0.04 | 0.27 | 0.08 | 0.06 | 0.09 | 0.11 | 0.06 | 0.09 | 0.13 | 0.08 | 0.09 | 0.09 | 0.02 | 0.12 | 0.00 | 0.17 | 0.06 | 0.05 | 0.02 | 0.31 | 0.00 | 1.03 | 0.06 | 0.17 | 0.01 | 0.13 | 0.00 | 0.00 | 0.04 | 0.19 | 0.25 | 0.37 | 0.08 | 0.10 | 0.05 | 0.12 | 0.08 | 0.25 | 0.17 | 0.29 | 0.10 | 0.12 | 0.02 | 0.01 | 0.00 | 0.22 | 0.01 | 0.04 | 0.03 | 0.19 | 0.00 | 0.08 | 0.06 | 0.12 |
| NR3C2 | ENSG00000151623 | 0.01 | 0.02 | 0.00 | 0.01 | 0.06 | 0.00 | 0.02 | 0.02 | 0.12 | 0.09 | 0.00 | 0.01 | 0.00 | 0.01 | 0.03 | 0.04 | 0.02 | 0.10 | 0.04 | 0.05 | 0.15 | 0.09 | 0.07 | 0.06 | 0.01 | 0.04 | 0.04 | 0.03 | 0.00 | 0.02 | 0.06 | 0.06 | 0.00 | 0.17 | 0.10 | 0.05 | 0.00 | 0.02 | 0.00 | 0.00 | 0.06 | 0.05 | 0.11 | 0.22 | 0.03 | 0.07 | 0.02 | 0.03 | 0.13 | 0.04 | 0.14 | 0.08 | 0.00 | 0.01 | 0.00 | 0.00 | 0.03 | 0.03 | 0.01 | 0.09 | 0.00 | 0.06 | 0.00 | 0.00 | 0.04 | 0.04 |
| EP300 | ENSG00000100393 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.12 | 0.00 | 0.03 | 0.00 | 0.04 | 0.04 | 0.03 | 0.06 | 0.02 | 0.03 | 0.01 | 0.03 | 0.00 | 0.02 | 0.01 | 0.01 | 0.02 | 0.01 | 0.05 | 0.05 | 0.03 | 0.03 | 0.02 | 0.04 | 0.01 | 0.04 | 0.00 | 0.00 | 0.06 | 0.00 | 0.00 | 0.03 | 0.03 | 0.02 | 0.25 | 0.04 | 0.07 | 0.05 | 0.05 | 0.17 | 0.15 | 0.08 | 0.05 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.05 | 0.00 | 0.00 | 0.33 | 0.00 |
| MAP3K8 | ENSG00000107968 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.03 | 0.07 | 0.00 | 0.01 | 0.02 | 0.02 | 0.07 | 0.02 | 0.04 | 0.02 | 0.03 | 0.02 | 0.07 | 0.01 | 0.08 | 0.03 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.03 | 0.16 | 0.04 | 0.00 | 0.01 | 0.02 | 0.01 | 0.11 | 0.00 | 0.03 | 0.02 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.03 | 0.02 |
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