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 |
| PTGS2 | ENSG00000073756 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.03 | 0.23 | 0.04 | 0.02 | 0.00 | 0.10 | 0.03 | 0.10 | 0.00 | 0.14 | 0.01 | 0.06 | 0.01 | 0.18 | 0.03 | 0.08 | 0.01 | 0.04 | 0.01 | 0.15 | 0.01 | 0.04 | 0.00 | 0.15 | 0.02 | 0.20 | 0.01 | 0.02 | 0.05 | 0.01 | 0.00 | 0.01 | 0.00 | 0.16 | 0.01 | 0.32 | 0.04 | 0.09 | 0.00 | 0.06 | 0.01 | 0.20 | 0.06 | 0.23 | 0.06 | 0.07 | 0.00 | 0.01 | 0.00 | 0.30 | 0.02 | 0.00 | 0.01 | 0.01 | 0.01 | 0.04 | 0.00 | 0.12 | 0.02 |
| TSG101 | ENSG00000074319 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.03 | 0.01 | 0.01 | 0.02 | 0.07 | 0.00 | 0.00 | 0.02 | 0.05 | 0.02 | 0.04 | 0.06 | 0.07 | 0.01 | 0.04 | 0.04 | 0.03 | 0.02 | 0.02 | 0.02 | 0.00 | 0.01 | 0.01 | 0.00 | 0.02 | 0.04 | 0.01 | 0.00 | 0.03 | 0.00 | 0.02 | 0.06 | 0.04 | 0.00 | 0.00 | 0.07 | 0.05 | 0.06 | 0.24 | 0.01 | 0.04 | 0.03 | 0.03 | 0.01 | 0.04 | 0.09 | 0.07 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.01 | 0.01 | 0.00 | 0.00 | 0.03 | 0.01 |
| CA12 | ENSG00000074410 | 0.00 | 0.00 | 0.00 | 0.01 | 0.19 | 0.00 | 0.01 | 0.02 | 0.03 | 0.03 | 0.00 | 0.00 | 0.08 | 0.00 | 0.04 | 0.03 | 0.05 | 0.02 | 0.02 | 0.02 | 0.03 | 0.03 | 0.05 | 0.04 | 0.01 | 0.02 | 0.00 | 0.02 | 0.02 | 0.01 | 0.02 | 0.01 | 0.00 | 0.01 | 0.04 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.05 | 0.13 | 0.11 | 0.05 | 0.01 | 0.05 | 0.05 | 0.07 | 0.19 | 0.12 | 0.03 | 0.01 | 0.02 | 0.00 | 0.00 | 0.06 | 0.00 | 0.01 | 0.01 | 0.01 | 0.04 | 0.00 | 0.00 | 0.03 | 0.02 |
| MGLL | ENSG00000074416 | 0.01 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.07 | 0.02 | 0.05 | 0.02 | 0.00 | 0.01 | 0.00 | 0.03 | 0.04 | 0.01 | 0.11 | 0.01 | 0.06 | 0.00 | 0.11 | 0.04 | 0.06 | 0.02 | 0.00 | 0.00 | 0.02 | 0.01 | 0.02 | 0.00 | 0.02 | 0.01 | 0.00 | 0.05 | 0.03 | 0.02 | 0.00 | 0.05 | 0.00 | 0.00 | 0.04 | 0.04 | 0.25 | 0.04 | 0.09 | 0.00 | 0.06 | 0.01 | 0.15 | 0.07 | 0.06 | 0.07 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.00 | 0.06 | 0.00 | 0.00 | 0.02 | 0.04 |
| MYDGF | ENSG00000074842 | 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 |
| TUBE1 | ENSG00000074935 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.28 | 0.02 | 0.12 | 0.00 | 0.01 | 0.00 | 0.14 | 0.02 | 0.05 | 0.05 | 0.04 | 0.02 | 0.03 | 0.04 | 0.08 | 0.05 | 0.07 | 0.01 | 0.03 | 0.02 | 0.04 | 0.00 | 0.04 | 0.00 | 0.08 | 0.00 | 0.12 | 0.04 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.12 | 0.09 | 0.08 | 0.25 | 0.01 | 0.02 | 0.05 | 0.02 | 0.17 | 0.02 | 0.21 | 0.06 | 0.00 | 0.04 | 0.00 | 0.00 | 0.01 | 0.21 | 0.01 | 0.02 | 0.01 | 0.07 | 0.00 | 0.03 | 0.01 | 0.14 |
| TXK | ENSG00000074966 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.02 | 0.05 | 0.04 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.09 | 0.02 | 0.17 | 0.03 | 0.06 | 0.02 | 0.10 | 0.04 | 0.04 | 0.04 | 0.03 | 0.01 | 0.01 | 0.03 | 0.02 | 0.02 | 0.04 | 0.03 | 0.00 | 0.14 | 0.04 | 0.03 | 0.00 | 0.02 | 0.00 | 0.00 | 0.05 | 0.01 | 0.15 | 0.03 | 0.01 | 0.02 | 0.03 | 0.01 | 0.06 | 0.00 | 0.11 | 0.07 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.01 | 0.05 | 0.04 | 0.02 | 0.02 |
| TACR2 | ENSG00000075073 | 0.00 | 0.01 | 0.00 | 0.01 | 0.03 | 0.00 | 0.02 | 0.04 | 0.02 | 0.03 | 0.00 | 0.00 | 0.01 | 0.00 | 0.04 | 0.02 | 0.06 | 0.03 | 0.03 | 0.02 | 0.05 | 0.06 | 0.08 | 0.02 | 0.03 | 0.03 | 0.08 | 0.04 | 0.01 | 0.00 | 0.02 | 0.03 | 0.25 | 0.04 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.06 | 0.03 | 0.11 | 0.11 | 0.00 | 0.01 | 0.06 | 0.03 | 0.18 | 0.05 | 0.02 | 0.12 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.01 | 0.02 | 0.00 | 0.00 | 0.00 | 0.01 |
| WNT8B | ENSG00000075290 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.10 | 0.01 | 0.09 | 0.00 | 0.02 | 0.00 | 0.16 | 0.01 | 0.03 | 0.03 | 0.07 | 0.00 | 0.06 | 0.02 | 0.07 | 0.02 | 0.09 | 0.01 | 0.10 | 0.00 | 0.07 | 0.01 | 0.03 | 0.02 | 0.06 | 0.11 | 0.14 | 0.01 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.03 | 0.08 | 0.07 | 0.33 | 0.01 | 0.07 | 0.03 | 0.09 | 0.08 | 0.09 | 0.02 | 0.04 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.07 | 0.02 | 0.04 | 0.00 | 0.05 | 0.00 | 0.00 | 0.02 | 0.04 |
| SLC25A40 | ENSG00000075303 | 0.01 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.04 | 0.00 | 0.05 | 0.01 | 0.00 | 0.00 | 0.03 | 0.03 | 0.03 | 0.01 | 0.21 | 0.02 | 0.19 | 0.01 | 0.50 | 0.02 | 0.24 | 0.01 | 0.03 | 0.01 | 0.01 | 0.00 | 0.05 | 0.00 | 0.06 | 0.03 | 0.04 | 0.01 | 0.10 | 0.02 | 0.00 | 0.02 | 0.00 | 0.00 | 0.06 | 0.02 | 0.19 | 0.05 | 0.09 | 0.02 | 0.02 | 0.02 | 0.09 | 0.06 | 0.06 | 0.05 | 0.13 | 0.00 | 0.00 | 0.00 | 0.13 | 0.00 | 0.02 | 0.00 | 0.05 | 0.01 | 0.00 | 0.00 | 0.02 | 0.02 |
| FGF4 | ENSG00000075388 | 0.01 | 0.01 | 0.03 | 0.01 | 0.09 | 0.00 | 0.10 | 0.00 | 0.80 | 0.01 | 0.00 | 0.00 | 0.08 | 0.00 | 0.21 | 0.00 | 1.09 | 0.01 | 1.94 | 0.01 | 2.78 | 0.00 | 0.43 | 0.02 | 0.02 | 0.01 | 0.09 | 0.01 | 0.04 | 0.01 | 0.43 | 0.01 | 0.76 | 0.02 | 0.03 | 0.01 | 0.02 | 0.00 | 0.00 | 0.00 | 1.24 | 0.02 | 0.42 | 0.03 | 0.30 | 0.03 | 0.16 | 0.02 | 0.19 | 0.11 | 0.19 | 0.05 | 0.00 | 0.05 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.01 | 0.01 | 0.03 | 0.00 | 0.00 | 0.39 | 0.01 |
| CACNG5 | ENSG00000075429 | 0.02 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.23 | 0.01 | 0.02 | 0.00 | 0.12 | 0.00 | 0.16 | 0.01 | 0.19 | 0.00 | 0.07 | 0.02 | 0.24 | 0.04 | 0.11 | 0.03 | 0.09 | 0.01 | 0.10 | 0.01 | 0.06 | 0.10 | 0.21 | 0.01 | 0.12 | 0.01 | 0.15 | 0.09 | 0.02 | 0.01 | 0.00 | 0.00 | 0.55 | 0.01 | 0.25 | 0.04 | 0.17 | 0.02 | 0.12 | 0.02 | 0.45 | 0.02 | 0.20 | 0.04 | 0.02 | 0.00 | 0.00 | 0.00 | 0.05 | 0.07 | 0.06 | 0.00 | 0.03 | 0.00 | 0.17 | 0.01 | 0.24 | 0.01 |
| ATP12A | ENSG00000075673 | 0.02 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.04 | 0.10 | 0.05 | 0.00 | 0.02 | 0.00 | 0.17 | 0.01 | 0.11 | 0.02 | 0.12 | 0.02 | 0.15 | 0.05 | 0.09 | 0.07 | 0.04 | 0.23 | 0.00 | 0.20 | 0.02 | 0.00 | 0.00 | 0.03 | 0.12 | 0.00 | 0.15 | 0.00 | 0.09 | 0.00 | 0.00 | 0.00 | 0.01 | 0.08 | 0.07 | 0.11 | 0.18 | 0.04 | 0.14 | 0.02 | 0.05 | 0.01 | 0.16 | 0.13 | 0.18 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.09 | 0.00 | 0.06 | 0.01 | 0.06 | 0.00 | 0.00 | 0.05 | 0.03 |
| TUBA3D | ENSG00000075886 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.16 | 0.04 | 0.03 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 | 0.06 | 0.02 | 0.04 | 0.01 | 0.08 | 0.07 | 0.03 | 0.05 | 0.01 | 0.02 | 0.00 | 0.01 | 0.02 | 0.01 | 0.01 | 0.04 | 0.00 | 0.03 | 0.05 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.06 | 0.08 | 0.17 | 0.04 | 0.01 | 0.02 | 0.01 | 0.07 | 0.00 | 0.10 | 0.04 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.12 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 |
| SLC46A1 | ENSG00000076351 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.01 | 0.24 | 0.01 | 0.08 | 0.01 | 0.00 | 0.03 | 0.07 | 0.01 | 0.12 | 0.02 | 0.05 | 0.02 | 0.15 | 0.01 | 0.13 | 0.01 | 0.09 | 0.01 | 0.09 | 0.01 | 0.03 | 0.01 | 0.04 | 0.00 | 0.02 | 0.01 | 0.02 | 0.05 | 0.00 | 0.14 | 0.00 | 0.00 | 0.31 | 0.03 | 0.16 | 0.06 | 0.02 | 0.03 | 0.16 | 0.03 | 0.19 | 0.05 | 0.07 | 0.15 | 0.00 | 0.01 | 0.00 | 0.02 | 0.06 | 0.00 | 0.00 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.02 | 0.03 |
| MCAM | ENSG00000076706 | 0.01 | 0.01 | 0.00 | 0.05 | 0.02 | 0.02 | 0.01 | 0.08 | 0.03 | 0.12 | 0.00 | 0.00 | 0.11 | 0.06 | 0.05 | 0.08 | 0.05 | 0.09 | 0.04 | 0.16 | 0.03 | 0.12 | 0.06 | 0.07 | 0.00 | 0.01 | 0.00 | 0.05 | 0.01 | 0.02 | 0.00 | 0.10 | 0.00 | 0.17 | 0.03 | 0.05 | 0.00 | 0.06 | 0.00 | 0.00 | 0.02 | 0.22 | 0.16 | 0.14 | 0.04 | 0.31 | 0.05 | 0.05 | 0.11 | 0.17 | 0.04 | 0.24 | 0.00 | 0.15 | 0.03 | 0.01 | 0.13 | 0.05 | 0.06 | 0.01 | 0.02 | 0.01 | 0.01 | 0.07 | 0.00 | 0.27 |
| DNAJC10 | ENSG00000077232 | 0.02 | 0.01 | 0.08 | 0.00 | 0.00 | 0.00 | 0.01 | 0.07 | 0.06 | 0.05 | 0.00 | 0.00 | 0.00 | 0.03 | 0.06 | 0.01 | 0.16 | 0.03 | 0.15 | 0.01 | 0.14 | 0.03 | 0.06 | 0.05 | 0.01 | 0.01 | 0.02 | 0.02 | 0.03 | 0.01 | 0.04 | 0.03 | 0.00 | 0.05 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.02 | 0.37 | 0.05 | 0.12 | 0.03 | 0.08 | 0.01 | 0.08 | 0.00 | 0.03 | 0.07 | 0.04 | 0.00 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.03 | 0.02 |
| JADE1 | ENSG00000077684 | 0.00 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.09 | 0.02 | 0.07 | 0.00 | 0.00 | 0.00 | 0.03 | 0.03 | 0.05 | 0.03 | 0.07 | 0.03 | 0.04 | 0.01 | 0.07 | 0.02 | 0.06 | 0.01 | 0.03 | 0.02 | 0.02 | 0.00 | 0.02 | 0.03 | 0.05 | 0.00 | 0.09 | 0.08 | 0.06 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.05 | 0.06 | 0.21 | 0.02 | 0.04 | 0.01 | 0.03 | 0.04 | 0.07 | 0.06 | 0.08 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.05 | 0.00 | 0.03 | 0.00 | 0.00 | 0.02 | 0.03 |
| FKBP6 | ENSG00000077800 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.04 | 0.00 | 0.04 | 0.02 | 0.00 | 0.00 | 0.02 | 0.00 | 0.02 | 0.02 | 0.10 | 0.02 | 0.05 | 0.03 | 0.17 | 0.03 | 0.10 | 0.02 | 0.01 | 0.00 | 0.01 | 0.00 | 0.02 | 0.01 | 0.06 | 0.01 | 0.00 | 0.01 | 0.17 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.09 | 0.02 | 0.16 | 0.06 | 0.04 | 0.01 | 0.05 | 0.02 | 0.08 | 0.00 | 0.06 | 0.03 | 0.12 | 0.00 | 0.00 | 0.00 | 0.10 | 0.00 | 0.02 | 0.01 | 0.05 | 0.00 | 0.00 | 0.00 | 0.06 | 0.02 |
| CST7 | ENSG00000077984 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.01 | 0.02 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.07 | 0.02 | 0.07 | 0.03 | 0.06 | 0.02 | 0.10 | 0.03 | 0.05 | 0.01 | 0.06 | 0.00 | 0.04 | 0.02 | 0.02 | 0.00 | 0.01 | 0.00 | 0.06 | 0.01 | 0.04 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.04 | 0.04 | 0.10 | 0.03 | 0.06 | 0.02 | 0.02 | 0.01 | 0.03 | 0.01 | 0.08 | 0.02 | 0.01 | 0.00 | 0.01 | 0.00 | 0.04 | 0.02 | 0.00 | 0.02 | 0.01 | 0.01 | 0.00 | 0.00 | 0.02 | 0.02 |
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