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 |
| YBX1 | ENSG00000065978 | 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 | 0.12 | 0.02 | 0.10 | 0.02 | 0.08 | 0.01 | 0.14 | 0.01 | 0.05 | 0.03 | 0.04 | 0.01 | 0.02 | 0.01 | 0.06 | 0.00 | 0.02 | 0.09 | 0.00 | 0.22 | 0.00 | 0.03 | 0.02 | 0.08 | 0.00 | 0.00 | 0.11 | 0.04 | 0.62 | 0.06 | 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 |
| CD84 | ENSG00000066294 | 0.03 | 0.00 | 0.01 | 0.01 | 0.00 | 0.03 | 0.02 | 0.04 | 0.78 | 0.00 | 0.02 | 0.00 | 0.10 | 0.02 | 0.27 | 0.00 | 0.29 | 0.00 | 0.06 | 0.00 | 0.27 | 0.01 | 0.14 | 0.00 | 0.03 | 0.00 | 0.11 | 0.00 | 0.06 | 0.00 | 0.29 | 0.00 | 0.30 | 0.01 | 0.16 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.30 | 0.01 | 0.40 | 0.02 | 0.16 | 0.00 | 0.14 | 0.00 | 0.37 | 0.00 | 0.45 | 0.02 | 0.10 | 0.00 | 0.00 | 0.00 | 0.24 | 0.02 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.18 | 0.01 |
| METTL22 | ENSG00000067365 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.26 | 0.06 | 0.00 | 0.00 | 0.06 | 0.00 | 0.05 | 0.02 | 0.06 | 0.05 | 0.05 | 0.01 | 0.05 | 0.05 | 0.05 | 0.04 | 0.00 | 0.02 | 0.00 | 0.02 | 0.01 | 0.00 | 0.02 | 0.01 | 0.00 | 0.05 | 0.06 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.07 | 0.01 | 0.14 | 0.15 | 0.16 | 0.01 | 0.03 | 0.02 | 0.09 | 0.05 | 0.10 | 0.02 | 0.02 | 0.00 | 0.00 | 0.00 | 0.05 | 0.00 | 0.01 | 0.00 | 0.02 | 0.02 | 0.00 | 0.00 | 0.04 | 0.01 |
| IARS2 | ENSG00000067704 | 0.01 | 0.02 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.06 | 0.09 | 0.06 | 0.02 | 0.02 | 0.05 | 0.01 | 0.08 | 0.01 | 0.12 | 0.01 | 0.05 | 0.00 | 0.20 | 0.03 | 0.06 | 0.01 | 0.03 | 0.00 | 0.06 | 0.02 | 0.00 | 0.01 | 0.13 | 0.02 | 0.16 | 0.02 | 0.08 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.22 | 0.02 | 0.28 | 0.12 | 0.06 | 0.01 | 0.07 | 0.02 | 0.16 | 0.00 | 0.05 | 0.21 | 0.02 | 0.03 | 0.01 | 0.00 | 0.07 | 0.11 | 0.00 | 0.02 | 0.01 | 0.06 | 0.09 | 0.00 | 0.11 | 0.03 |
| PDK3 | ENSG00000067992 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.04 | 0.01 | 0.06 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.04 | 0.11 | 0.03 | 0.02 | 0.02 | 0.11 | 0.04 | 0.06 | 0.01 | 0.00 | 0.01 | 0.09 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.06 | 0.01 | 0.02 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.08 | 0.02 | 0.09 | 0.16 | 0.08 | 0.00 | 0.04 | 0.02 | 0.11 | 0.11 | 0.19 | 0.03 | 0.05 | 0.00 | 0.00 | 0.00 | 0.09 | 0.02 | 0.01 | 0.02 | 0.02 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 |
| HYAL2 | ENSG00000068001 | 0.00 | 0.18 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.02 | 0.03 | 0.17 | 0.02 | 0.00 | 0.00 | 0.54 | 0.01 | 0.06 | 0.00 | 0.11 | 0.00 | 0.06 | 0.04 | 0.14 | 0.01 | 0.11 | 0.00 | 0.05 | 0.01 | 0.06 | 0.00 | 0.04 | 0.04 | 0.06 | 0.00 | 0.20 | 0.01 | 0.02 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.17 | 0.06 | 0.19 | 0.00 | 0.06 | 0.08 | 0.06 | 0.10 | 0.36 | 0.03 | 0.17 | 0.02 | 0.03 | 0.00 | 0.01 | 0.00 | 0.06 | 0.01 | 0.06 | 0.01 | 0.04 | 0.00 | 0.03 | 0.01 | 0.04 |
| PYGM | ENSG00000068976 | 0.01 | 0.00 | 0.00 | 0.01 | 0.07 | 0.00 | 0.03 | 0.01 | 0.11 | 0.01 | 0.00 | 0.00 | 0.08 | 0.00 | 0.06 | 0.03 | 0.07 | 0.02 | 0.18 | 0.02 | 0.11 | 0.04 | 0.03 | 0.03 | 0.01 | 0.01 | 0.04 | 0.03 | 0.00 | 0.02 | 0.01 | 0.03 | 0.00 | 0.07 | 0.08 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.08 | 0.08 | 0.17 | 0.04 | 0.12 | 0.01 | 0.08 | 0.03 | 0.22 | 0.04 | 0.09 | 0.03 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.05 | 0.05 |
| TRPC7 | ENSG00000069018 | 0.28 | 0.01 | 0.02 | 0.01 | 0.00 | 0.00 | 0.02 | 0.03 | 0.04 | 0.04 | 0.00 | 0.00 | 0.00 | 0.04 | 0.00 | 0.07 | 0.01 | 0.05 | 0.01 | 0.04 | 0.03 | 0.05 | 0.02 | 0.08 | 0.01 | 0.03 | 0.02 | 0.03 | 0.01 | 0.03 | 0.06 | 0.04 | 0.09 | 0.01 | 0.24 | 0.02 | 0.00 | 0.06 | 0.01 | 0.00 | 0.03 | 0.03 | 0.12 | 0.14 | 0.03 | 0.02 | 0.01 | 0.01 | 0.10 | 0.01 | 0.08 | 0.05 | 0.00 | 0.00 | 0.00 | 0.10 | 0.04 | 0.00 | 0.00 | 0.03 | 0.01 | 0.02 | 0.00 | 0.03 | 0.04 | 0.10 |
| GAL | ENSG00000069482 | 0.01 | 0.00 | 0.03 | 0.01 | 0.08 | 0.02 | 0.09 | 0.01 | 0.31 | 0.01 | 0.00 | 0.00 | 0.08 | 0.00 | 0.18 | 0.01 | 0.38 | 0.02 | 0.73 | 0.01 | 1.25 | 0.02 | 0.19 | 0.03 | 0.01 | 0.01 | 0.02 | 0.02 | 0.03 | 0.02 | 0.22 | 0.01 | 0.44 | 0.05 | 0.00 | 0.01 | 0.03 | 0.00 | 0.00 | 0.00 | 0.55 | 0.04 | 0.36 | 0.04 | 0.22 | 0.01 | 0.12 | 0.02 | 0.18 | 0.10 | 0.10 | 0.06 | 0.00 | 0.05 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.01 | 0.01 | 0.04 | 0.00 | 0.00 | 0.31 | 0.02 |
| MAOB | ENSG00000069535 | 0.01 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 | 0.03 | 0.03 | 0.00 | 0.00 | 0.00 | 0.02 | 0.08 | 0.02 | 0.05 | 0.04 | 0.02 | 0.03 | 0.09 | 0.06 | 0.03 | 0.01 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.02 | 0.02 | 0.01 | 0.00 | 0.01 | 0.13 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.04 | 0.01 | 0.15 | 0.08 | 0.01 | 0.03 | 0.04 | 0.01 | 0.29 | 0.05 | 0.10 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.08 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.02 | 0.00 |
| DRD4 | ENSG00000069696 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.03 | 0.01 | 0.02 | 0.01 | 0.14 | 0.00 | 0.00 | 0.02 | 0.05 | 0.03 | 0.08 | 0.02 | 0.16 | 0.03 | 0.07 | 0.04 | 0.15 | 0.03 | 0.07 | 0.01 | 0.02 | 0.01 | 0.03 | 0.03 | 0.06 | 0.06 | 0.04 | 0.03 | 0.01 | 0.05 | 0.09 | 0.02 | 0.06 | 0.00 | 0.00 | 0.03 | 0.13 | 0.06 | 0.50 | 0.01 | 0.07 | 0.05 | 0.09 | 0.04 | 0.18 | 0.02 | 0.22 | 0.03 | 0.07 | 0.00 | 0.00 | 0.05 | 0.00 | 0.01 | 0.11 | 0.01 | 0.06 | 0.00 | 0.00 | 0.02 | 0.04 |
| PLA2G10 | ENSG00000069764 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.11 | 0.06 | 0.00 | 0.00 | 0.03 | 0.02 | 0.03 | 0.02 | 0.05 | 0.03 | 0.03 | 0.02 | 0.04 | 0.03 | 0.05 | 0.02 | 0.02 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.05 | 0.02 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.05 | 0.02 | 0.19 | 0.07 | 0.09 | 0.00 | 0.05 | 0.01 | 0.16 | 0.00 | 0.08 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.09 | 0.00 | 0.01 | 0.01 | 0.01 | 0.02 | 0.00 | 0.00 | 0.04 | 0.01 |
| SCT | ENSG00000070031 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.03 | 0.01 | 0.02 | 0.01 | 0.14 | 0.00 | 0.00 | 0.02 | 0.05 | 0.03 | 0.08 | 0.02 | 0.16 | 0.03 | 0.07 | 0.04 | 0.15 | 0.03 | 0.07 | 0.01 | 0.03 | 0.01 | 0.03 | 0.03 | 0.06 | 0.06 | 0.04 | 0.03 | 0.01 | 0.05 | 0.10 | 0.02 | 0.06 | 0.00 | 0.00 | 0.03 | 0.13 | 0.06 | 0.50 | 0.01 | 0.07 | 0.05 | 0.09 | 0.18 | 0.18 | 0.02 | 0.22 | 0.03 | 0.07 | 0.00 | 0.00 | 0.05 | 0.00 | 0.01 | 0.11 | 0.01 | 0.07 | 0.00 | 0.00 | 0.02 | 0.03 |
| SLC44A1 | ENSG00000070214 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.04 | 0.01 | 0.05 | 0.05 | 0.00 | 0.01 | 0.02 | 0.05 | 0.03 | 0.02 | 0.06 | 0.01 | 0.06 | 0.00 | 0.09 | 0.04 | 0.04 | 0.04 | 0.00 | 0.01 | 0.04 | 0.03 | 0.00 | 0.01 | 0.03 | 0.04 | 0.00 | 0.08 | 0.06 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.05 | 0.09 | 0.15 | 0.02 | 0.02 | 0.01 | 0.05 | 0.00 | 0.19 | 0.10 | 0.01 | 0.04 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.01 | 0.00 | 0.00 | 0.02 | 0.02 |
| FGF22 | ENSG00000070388 | 0.00 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.02 | 0.02 | 0.14 | 0.05 | 0.00 | 0.03 | 0.09 | 0.03 | 0.09 | 0.03 | 0.15 | 0.01 | 0.15 | 0.05 | 0.18 | 0.04 | 0.07 | 0.01 | 0.06 | 0.02 | 0.09 | 0.01 | 0.07 | 0.03 | 0.12 | 0.04 | 0.03 | 0.12 | 0.01 | 0.03 | 0.01 | 0.00 | 0.01 | 0.02 | 0.17 | 0.03 | 0.91 | 0.05 | 0.23 | 0.03 | 0.25 | 0.00 | 0.84 | 0.23 | 0.21 | 0.01 | 0.01 | 0.00 | 0.02 | 0.03 | 0.00 | 0.07 | 0.02 | 0.08 | 0.01 | 0.01 | 0.03 | 0.02 | 0.08 |
| FSTL3 | ENSG00000070404 | 0.00 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.02 | 0.02 | 0.14 | 0.05 | 0.00 | 0.03 | 0.09 | 0.03 | 0.09 | 0.03 | 0.15 | 0.01 | 0.15 | 0.05 | 0.18 | 0.05 | 0.07 | 0.01 | 0.06 | 0.02 | 0.09 | 0.01 | 0.07 | 0.02 | 0.12 | 0.04 | 0.03 | 0.12 | 0.01 | 0.01 | 0.01 | 0.00 | 0.01 | 0.02 | 0.17 | 0.03 | 0.91 | 0.05 | 0.23 | 0.03 | 0.25 | 0.00 | 0.84 | 0.27 | 0.21 | 0.01 | 0.01 | 0.00 | 0.02 | 0.03 | 0.00 | 0.08 | 0.01 | 0.08 | 0.01 | 0.01 | 0.03 | 0.02 | 0.08 |
| CHAT | ENSG00000070748 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.04 | 0.07 | 0.07 | 0.00 | 0.00 | 0.01 | 0.04 | 0.04 | 0.03 | 0.07 | 0.03 | 0.05 | 0.03 | 0.09 | 0.09 | 0.03 | 0.02 | 0.00 | 0.03 | 0.02 | 0.01 | 0.00 | 0.01 | 0.01 | 0.02 | 0.09 | 0.01 | 0.02 | 0.02 | 0.00 | 0.00 | 0.00 | 0.01 | 0.06 | 0.05 | 0.07 | 0.14 | 0.01 | 0.02 | 0.03 | 0.03 | 0.03 | 0.03 | 0.07 | 0.12 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.04 |
| CSNK2A2 | ENSG00000070770 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.05 | 0.01 | 0.03 | 0.00 | 0.00 | 0.00 | 0.01 | 0.04 | 0.03 | 0.03 | 0.01 | 0.03 | 0.02 | 0.10 | 0.01 | 0.02 | 0.03 | 0.02 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.01 | 0.02 | 0.00 | 0.01 | 0.06 | 0.06 | 0.00 | 0.02 | 0.00 | 0.00 | 0.02 | 0.04 | 0.04 | 0.15 | 0.00 | 0.06 | 0.03 | 0.07 | 0.02 | 0.16 | 0.03 | 0.05 | 0.12 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.01 | 0.00 | 0.02 | 0.00 | 0.03 | 0.02 | 0.04 |
| CDC42 | ENSG00000070831 | 0.00 | 0.05 | 0.00 | 0.08 | 0.00 | 0.00 | 0.01 | 0.03 | 0.08 | 0.09 | 0.00 | 0.01 | 0.04 | 0.23 | 0.04 | 0.06 | 0.05 | 0.11 | 0.03 | 0.07 | 0.03 | 0.10 | 0.07 | 0.12 | 0.00 | 0.16 | 0.00 | 0.21 | 0.01 | 0.08 | 0.01 | 0.22 | 0.00 | 1.06 | 0.08 | 0.04 | 0.01 | 0.10 | 0.00 | 0.00 | 0.02 | 0.19 | 0.10 | 0.44 | 0.05 | 0.09 | 0.06 | 0.13 | 0.17 | 0.19 | 0.17 | 0.10 | 0.05 | 0.06 | 0.02 | 0.00 | 0.00 | 0.11 | 0.00 | 0.02 | 0.02 | 0.11 | 0.00 | 0.12 | 0.06 | 0.08 |
| EPHA8 | ENSG00000070886 | 0.00 | 0.05 | 0.00 | 0.08 | 0.00 | 0.00 | 0.01 | 0.03 | 0.08 | 0.09 | 0.00 | 0.03 | 0.04 | 0.23 | 0.04 | 0.06 | 0.05 | 0.11 | 0.03 | 0.07 | 0.06 | 0.10 | 0.06 | 0.11 | 0.00 | 0.16 | 0.02 | 0.21 | 0.01 | 0.08 | 0.01 | 0.21 | 0.00 | 1.06 | 0.01 | 0.06 | 0.01 | 0.10 | 0.00 | 0.00 | 0.01 | 0.19 | 0.12 | 0.44 | 0.04 | 0.08 | 0.04 | 0.13 | 0.12 | 0.19 | 0.20 | 0.10 | 0.05 | 0.06 | 0.02 | 0.00 | 0.00 | 0.11 | 0.04 | 0.02 | 0.04 | 0.11 | 0.00 | 0.12 | 0.08 | 0.08 |
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