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 |
| MAP3K7 | ENSG00000135341 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.36 | 0.02 | 0.08 | 0.00 | 0.00 | 0.02 | 0.04 | 0.01 | 0.06 | 0.06 | 0.03 | 0.02 | 0.03 | 0.08 | 0.06 | 0.03 | 0.08 | 0.00 | 0.02 | 0.01 | 0.02 | 0.00 | 0.03 | 0.01 | 0.07 | 0.00 | 0.11 | 0.12 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.05 | 0.11 | 0.16 | 0.13 | 0.03 | 0.01 | 0.02 | 0.01 | 0.16 | 0.05 | 0.07 | 0.13 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.20 | 0.01 | 0.01 | 0.00 | 0.04 | 0.04 | 0.03 | 0.01 | 0.04 |
| NPR3 | ENSG00000113389 | 0.00 | 0.00 | 0.01 | 0.00 | 0.03 | 0.03 | 0.02 | 0.01 | 0.09 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.19 | 0.00 | 0.20 | 0.01 | 0.07 | 0.00 | 0.10 | 0.01 | 0.12 | 0.02 | 0.03 | 0.01 | 0.03 | 0.00 | 0.02 | 0.00 | 0.05 | 0.00 | 0.00 | 0.01 | 0.32 | 0.02 | 0.01 | 0.01 | 0.00 | 0.00 | 0.06 | 0.02 | 0.18 | 0.02 | 0.07 | 0.00 | 0.06 | 0.01 | 0.15 | 0.03 | 0.20 | 0.01 | 0.00 | 0.02 | 0.00 | 0.01 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.15 | 0.02 |
| SMPD3 | ENSG00000103056 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.06 | 0.01 | 0.08 | 0.16 | 0.02 | 0.00 | 0.00 | 0.01 | 0.07 | 0.05 | 0.03 | 0.07 | 0.02 | 0.03 | 0.02 | 0.18 | 0.05 | 0.05 | 0.04 | 0.00 | 0.00 | 0.02 | 0.01 | 0.01 | 0.00 | 0.03 | 0.04 | 0.05 | 0.01 | 0.24 | 0.03 | 0.01 | 0.02 | 0.00 | 0.01 | 0.05 | 0.05 | 0.03 | 0.33 | 0.03 | 0.02 | 0.03 | 0.09 | 0.05 | 0.14 | 0.02 | 0.05 | 0.15 | 0.02 | 0.01 | 0.05 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.03 | 0.05 | 0.01 |
| ABCA6 | ENSG00000154262 | 0.02 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.03 | 0.03 | 0.22 | 0.00 | 0.02 | 0.00 | 0.13 | 0.00 | 0.16 | 0.00 | 0.20 | 0.01 | 0.07 | 0.02 | 0.25 | 0.03 | 0.13 | 0.02 | 0.05 | 0.01 | 0.07 | 0.03 | 0.05 | 0.10 | 0.22 | 0.01 | 0.12 | 0.01 | 0.15 | 0.12 | 0.02 | 0.01 | 0.00 | 0.00 | 0.43 | 0.02 | 0.27 | 0.04 | 0.17 | 0.03 | 0.10 | 0.01 | 0.34 | 0.02 | 0.23 | 0.04 | 0.03 | 0.00 | 0.00 | 0.00 | 0.05 | 0.00 | 0.07 | 0.00 | 0.02 | 0.01 | 0.17 | 0.01 | 0.22 | 0.01 |
| NFKB1 | ENSG00000109320 | 0.00 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.02 | 0.03 | 0.05 | 0.00 | 0.00 | 0.00 | 0.06 | 0.02 | 0.03 | 0.03 | 0.05 | 0.01 | 0.02 | 0.03 | 0.06 | 0.02 | 0.04 | 0.01 | 0.03 | 0.01 | 0.03 | 0.00 | 0.02 | 0.01 | 0.13 | 0.00 | 0.03 | 0.04 | 0.02 | 0.04 | 0.01 | 0.00 | 0.00 | 0.05 | 0.05 | 0.03 | 0.30 | 0.02 | 0.01 | 0.01 | 0.04 | 0.00 | 0.11 | 0.02 | 0.05 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.02 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.05 |
| PTGER3 | ENSG00000050628 | 0.00 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.06 | 0.05 | 0.05 | 0.00 | 0.02 | 0.00 | 0.06 | 0.05 | 0.06 | 0.05 | 0.05 | 0.01 | 0.06 | 0.02 | 0.06 | 0.02 | 0.04 | 0.00 | 0.10 | 0.01 | 0.05 | 0.00 | 0.01 | 0.02 | 0.04 | 0.00 | 0.12 | 0.04 | 0.01 | 0.00 | 0.18 | 0.00 | 0.00 | 0.05 | 0.07 | 0.14 | 0.15 | 0.03 | 0.04 | 0.02 | 0.03 | 0.00 | 0.06 | 0.19 | 0.04 | 0.01 | 0.03 | 0.02 | 0.01 | 0.00 | 0.03 | 0.00 | 0.01 | 0.02 | 0.03 | 0.03 | 0.05 | 0.03 | 0.06 |
| MUC1 | ENSG00000185499 | 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 |
| LYN | ENSG00000254087 | 0.00 | 0.01 | 0.00 | 0.00 | 0.06 | 0.00 | 0.05 | 0.01 | 0.10 | 0.03 | 0.00 | 0.00 | 0.00 | 0.07 | 0.13 | 0.03 | 0.13 | 0.03 | 0.05 | 0.01 | 0.07 | 0.03 | 0.07 | 0.02 | 0.07 | 0.02 | 0.10 | 0.01 | 0.01 | 0.01 | 0.03 | 0.02 | 0.00 | 0.02 | 0.02 | 0.00 | 0.01 | 0.02 | 0.00 | 0.00 | 0.16 | 0.02 | 0.44 | 0.02 | 0.03 | 0.01 | 0.11 | 0.00 | 0.83 | 0.12 | 0.14 | 0.05 | 0.21 | 0.00 | 0.01 | 0.00 | 0.04 | 0.07 | 0.00 | 0.00 | 0.00 | 0.01 | 0.20 | 0.00 | 0.06 | 0.01 |
| ATM | ENSG00000149311 | 0.00 | 0.01 | 0.00 | 0.06 | 0.09 | 0.02 | 0.03 | 0.10 | 0.08 | 0.11 | 0.00 | 0.00 | 0.02 | 0.12 | 0.04 | 0.09 | 0.06 | 0.08 | 0.04 | 0.15 | 0.06 | 0.13 | 0.04 | 0.08 | 0.01 | 0.03 | 0.01 | 0.08 | 0.01 | 0.01 | 0.03 | 0.08 | 0.00 | 0.18 | 0.00 | 0.08 | 0.01 | 0.05 | 0.00 | 0.00 | 0.03 | 0.22 | 0.19 | 0.17 | 0.04 | 0.27 | 0.02 | 0.06 | 0.07 | 0.25 | 0.08 | 0.20 | 0.01 | 0.10 | 0.02 | 0.00 | 0.07 | 0.02 | 0.01 | 0.01 | 0.01 | 0.01 | 0.00 | 0.04 | 0.01 | 0.26 |
| IL1R2 | ENSG00000115590 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.10 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.02 | 0.10 | 0.01 | 0.08 | 0.01 | 0.14 | 0.02 | 0.07 | 0.02 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.03 | 0.01 | 0.00 | 0.01 | 0.03 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.02 | 0.20 | 0.07 | 0.05 | 0.00 | 0.05 | 0.01 | 0.11 | 0.00 | 0.12 | 0.04 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.00 | 0.01 | 0.02 | 0.00 | 0.00 | 0.02 | 0.01 |
| APOB | ENSG00000084674 | 0.00 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 | 0.10 | 0.01 | 0.00 | 0.00 | 0.03 | 0.05 | 0.06 | 0.02 | 0.10 | 0.03 | 0.03 | 0.02 | 0.06 | 0.04 | 0.02 | 0.04 | 0.01 | 0.01 | 0.00 | 0.02 | 0.01 | 0.04 | 0.09 | 0.01 | 0.00 | 0.05 | 0.01 | 0.04 | 0.01 | 0.00 | 0.00 | 0.00 | 0.04 | 0.04 | 0.20 | 0.14 | 0.09 | 0.00 | 0.11 | 0.03 | 0.19 | 0.03 | 0.03 | 0.10 | 0.18 | 0.01 | 0.00 | 0.00 | 0.00 | 0.07 | 0.01 | 0.01 | 0.02 | 0.02 | 0.05 | 0.00 | 0.01 | 0.04 |
| ST3GAL4 | ENSG00000110080 | 0.00 | 0.01 | 0.00 | 0.05 | 0.00 | 0.05 | 0.02 | 0.06 | 0.03 | 0.10 | 0.00 | 0.00 | 0.11 | 0.07 | 0.05 | 0.09 | 0.04 | 0.10 | 0.04 | 0.14 | 0.12 | 0.13 | 0.05 | 0.08 | 0.02 | 0.02 | 0.01 | 0.03 | 0.01 | 0.02 | 0.01 | 0.09 | 0.00 | 0.23 | 0.02 | 0.06 | 0.01 | 0.05 | 0.00 | 0.00 | 0.05 | 0.22 | 0.22 | 0.17 | 0.04 | 0.32 | 0.06 | 0.08 | 0.05 | 0.19 | 0.01 | 0.27 | 0.00 | 0.28 | 0.04 | 0.00 | 0.13 | 0.02 | 0.06 | 0.01 | 0.01 | 0.01 | 0.00 | 0.07 | 0.01 | 0.26 |
| DPYD | ENSG00000188641 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.08 | 0.04 | 0.08 | 0.00 | 0.00 | 0.00 | 0.40 | 0.03 | 0.12 | 0.05 | 0.11 | 0.03 | 0.10 | 0.04 | 0.12 | 0.02 | 0.08 | 0.00 | 0.08 | 0.01 | 0.11 | 0.00 | 0.02 | 0.02 | 0.04 | 0.04 | 0.16 | 0.02 | 0.04 | 0.01 | 0.24 | 0.00 | 0.00 | 0.04 | 0.11 | 0.12 | 0.17 | 0.01 | 0.08 | 0.02 | 0.03 | 0.02 | 0.09 | 0.08 | 0.11 | 0.03 | 0.06 | 0.01 | 0.00 | 0.00 | 0.03 | 0.01 | 0.01 | 0.01 | 0.04 | 0.00 | 0.03 | 0.03 | 0.11 |
| PTPN3 | ENSG00000070159 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.05 | 0.05 | 0.00 | 0.00 | 0.02 | 0.02 | 0.04 | 0.02 | 0.05 | 0.01 | 0.06 | 0.01 | 0.10 | 0.01 | 0.03 | 0.04 | 0.00 | 0.01 | 0.05 | 0.03 | 0.00 | 0.01 | 0.01 | 0.06 | 0.00 | 0.08 | 0.08 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.05 | 0.08 | 0.12 | 0.02 | 0.01 | 0.02 | 0.05 | 0.00 | 0.15 | 0.11 | 0.02 | 0.04 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.02 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 |
| SLC2A1 | ENSG00000117394 | 0.00 | 0.02 | 0.01 | 0.03 | 0.00 | 0.00 | 0.00 | 0.02 | 0.19 | 0.03 | 0.00 | 0.00 | 0.08 | 0.03 | 0.11 | 0.02 | 0.11 | 0.02 | 0.08 | 0.02 | 0.14 | 0.01 | 0.05 | 0.03 | 0.04 | 0.01 | 0.02 | 0.01 | 0.03 | 0.00 | 0.03 | 0.09 | 0.00 | 0.22 | 0.06 | 0.03 | 0.02 | 0.08 | 0.00 | 0.00 | 0.10 | 0.04 | 0.63 | 0.05 | 0.10 | 0.01 | 0.12 | 0.01 | 0.13 | 0.05 | 0.12 | 0.04 | 0.05 | 0.03 | 0.02 | 0.00 | 0.00 | 0.05 | 0.00 | 0.01 | 0.02 | 0.01 | 0.00 | 0.07 | 0.05 | 0.02 |
| PLOD1 | ENSG00000083444 | 0.00 | 0.06 | 0.01 | 0.08 | 0.00 | 0.00 | 0.00 | 0.05 | 0.10 | 0.07 | 0.00 | 0.02 | 0.04 | 0.26 | 0.07 | 0.05 | 0.05 | 0.11 | 0.04 | 0.08 | 0.15 | 0.08 | 0.10 | 0.08 | 0.01 | 0.13 | 0.00 | 0.20 | 0.03 | 0.06 | 0.03 | 0.23 | 0.00 | 1.07 | 0.04 | 0.13 | 0.01 | 0.09 | 0.00 | 0.00 | 0.02 | 0.19 | 0.21 | 0.36 | 0.04 | 0.10 | 0.07 | 0.10 | 0.08 | 0.23 | 0.19 | 0.19 | 0.08 | 0.09 | 0.02 | 0.00 | 0.00 | 0.03 | 0.00 | 0.03 | 0.08 | 0.12 | 0.00 | 0.07 | 0.07 | 0.11 |
| GAK | ENSG00000178950 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.04 | 0.02 | 0.10 | 0.05 | 0.02 | 0.02 | 0.01 | 0.03 | 0.06 | 0.05 | 0.05 | 0.07 | 0.03 | 0.07 | 0.11 | 0.09 | 0.09 | 0.05 | 0.02 | 0.03 | 0.05 | 0.04 | 0.10 | 0.02 | 0.04 | 0.07 | 0.00 | 0.01 | 0.22 | 0.03 | 0.00 | 0.00 | 0.01 | 0.00 | 0.04 | 0.08 | 0.42 | 0.11 | 0.02 | 0.06 | 0.08 | 0.06 | 0.15 | 0.03 | 0.14 | 0.07 | 0.02 | 0.02 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.02 | 0.01 | 0.04 | 0.02 | 0.00 | 0.04 | 0.05 |
| RELN | ENSG00000189056 | 0.01 | 0.00 | 0.07 | 0.00 | 0.01 | 0.00 | 0.04 | 0.02 | 0.05 | 0.02 | 0.00 | 0.00 | 0.03 | 0.00 | 0.09 | 0.02 | 0.19 | 0.02 | 0.22 | 0.01 | 0.45 | 0.04 | 0.19 | 0.02 | 0.02 | 0.01 | 0.02 | 0.00 | 0.02 | 0.02 | 0.06 | 0.02 | 0.00 | 0.02 | 0.02 | 0.06 | 0.00 | 0.02 | 0.00 | 0.00 | 0.05 | 0.04 | 0.26 | 0.06 | 0.04 | 0.02 | 0.04 | 0.03 | 0.09 | 0.05 | 0.09 | 0.05 | 0.08 | 0.01 | 0.00 | 0.00 | 0.13 | 0.00 | 0.08 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.06 | 0.03 |
| AKR1C1 | ENSG00000187134 | 0.02 | 0.01 | 0.03 | 0.01 | 0.01 | 0.00 | 0.01 | 0.03 | 0.35 | 0.03 | 0.00 | 0.00 | 0.02 | 0.14 | 0.13 | 0.07 | 0.08 | 0.13 | 0.03 | 0.07 | 0.15 | 0.10 | 0.09 | 0.03 | 0.03 | 0.03 | 0.02 | 0.00 | 0.03 | 0.03 | 0.07 | 0.03 | 0.00 | 0.05 | 0.00 | 0.03 | 0.01 | 0.00 | 0.00 | 0.00 | 0.19 | 0.02 | 0.36 | 0.11 | 0.04 | 0.02 | 0.04 | 0.01 | 0.15 | 0.00 | 0.06 | 0.10 | 0.01 | 0.04 | 0.00 | 0.00 | 0.07 | 0.07 | 0.08 | 0.01 | 0.03 | 0.01 | 0.00 | 0.02 | 0.03 | 0.03 |
| AMPD2 | ENSG00000116337 | 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 | 0.13 | 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 |
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