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 |
| CPO | ENSG00000144410 | 0.02 | 0.04 | 0.04 | 0.02 | 0.00 | 0.03 | 0.01 | 0.02 | 0.02 | 0.16 | 0.00 | 0.00 | 0.00 | 0.08 | 0.04 | 0.02 | 0.07 | 0.13 | 0.03 | 0.16 | 0.06 | 0.10 | 0.07 | 0.03 | 0.02 | 0.01 | 0.02 | 0.01 | 0.07 | 0.02 | 0.07 | 0.02 | 0.00 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.04 | 0.21 | 0.11 | 0.03 | 0.29 | 0.04 | 0.04 | 0.06 | 0.05 | 0.04 | 0.12 | 0.06 | 0.01 | 0.00 | 0.00 | 0.00 | 0.04 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.02 | 0.02 | 0.03 |
| CTDSP1 | ENSG00000144579 | 0.02 | 0.07 | 0.04 | 0.04 | 0.00 | 0.03 | 0.02 | 0.01 | 0.01 | 0.26 | 0.00 | 0.00 | 0.00 | 0.12 | 0.02 | 0.03 | 0.05 | 0.19 | 0.01 | 0.18 | 0.03 | 0.13 | 0.07 | 0.04 | 0.02 | 0.01 | 0.02 | 0.02 | 0.05 | 0.03 | 0.04 | 0.05 | 0.00 | 0.01 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.04 | 0.06 | 0.20 | 0.16 | 0.05 | 0.34 | 0.08 | 0.04 | 0.12 | 0.05 | 0.08 | 0.21 | 0.08 | 0.01 | 0.00 | 0.00 | 0.00 | 0.04 | 0.01 | 0.02 | 0.00 | 0.00 | 0.02 | 0.02 | 0.02 | 0.03 |
| ACKR2 | ENSG00000144648 | 0.00 | 0.18 | 0.00 | 0.02 | 0.08 | 0.00 | 0.01 | 0.01 | 0.06 | 0.08 | 0.00 | 0.03 | 0.01 | 0.41 | 0.01 | 0.04 | 0.00 | 0.07 | 0.00 | 0.05 | 0.01 | 0.04 | 0.03 | 0.08 | 0.00 | 0.03 | 0.04 | 0.05 | 0.00 | 0.03 | 0.07 | 0.02 | 0.00 | 0.20 | 0.01 | 0.02 | 0.02 | 0.03 | 0.00 | 0.00 | 0.01 | 0.13 | 0.09 | 0.17 | 0.02 | 0.04 | 0.02 | 0.04 | 0.02 | 0.19 | 0.06 | 0.10 | 0.01 | 0.04 | 0.00 | 0.01 | 0.00 | 0.10 | 0.01 | 0.04 | 0.02 | 0.04 | 0.00 | 0.03 | 0.02 | 0.04 |
| SLC25A38 | ENSG00000144659 | 0.00 | 0.18 | 0.00 | 0.01 | 0.08 | 0.00 | 0.00 | 0.01 | 0.10 | 0.06 | 0.00 | 0.02 | 0.02 | 0.30 | 0.01 | 0.04 | 0.02 | 0.05 | 0.00 | 0.04 | 0.03 | 0.04 | 0.05 | 0.07 | 0.00 | 0.02 | 0.04 | 0.02 | 0.01 | 0.02 | 0.05 | 0.02 | 0.00 | 0.20 | 0.01 | 0.02 | 0.00 | 0.03 | 0.00 | 0.00 | 0.03 | 0.09 | 0.12 | 0.16 | 0.02 | 0.03 | 0.03 | 0.04 | 0.10 | 0.13 | 0.08 | 0.07 | 0.01 | 0.04 | 0.00 | 0.01 | 0.00 | 0.06 | 0.01 | 0.03 | 0.01 | 0.03 | 0.00 | 0.00 | 0.04 | 0.04 |
| SLC22A14 | ENSG00000144671 | 0.00 | 0.18 | 0.00 | 0.01 | 0.08 | 0.00 | 0.00 | 0.01 | 0.13 | 0.04 | 0.00 | 0.03 | 0.02 | 0.28 | 0.01 | 0.04 | 0.02 | 0.04 | 0.00 | 0.04 | 0.03 | 0.04 | 0.07 | 0.07 | 0.00 | 0.02 | 0.03 | 0.02 | 0.01 | 0.02 | 0.06 | 0.02 | 0.00 | 0.20 | 0.05 | 0.02 | 0.00 | 0.03 | 0.00 | 0.00 | 0.04 | 0.08 | 0.11 | 0.16 | 0.02 | 0.04 | 0.03 | 0.04 | 0.12 | 0.15 | 0.09 | 0.06 | 0.03 | 0.04 | 0.00 | 0.01 | 0.06 | 0.09 | 0.01 | 0.03 | 0.01 | 0.03 | 0.00 | 0.08 | 0.04 | 0.05 |
| SLC25A26 | ENSG00000144741 | 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 |
| ADGRG7 | ENSG00000144820 | 0.01 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.02 | 0.02 | 0.04 | 0.02 | 0.00 | 0.00 | 0.00 | 0.03 | 0.05 | 0.02 | 0.15 | 0.03 | 0.07 | 0.01 | 0.08 | 0.04 | 0.06 | 0.02 | 0.00 | 0.01 | 0.03 | 0.02 | 0.00 | 0.01 | 0.03 | 0.01 | 0.00 | 0.10 | 0.10 | 0.01 | 0.00 | 0.06 | 0.00 | 0.00 | 0.06 | 0.02 | 0.21 | 0.04 | 0.05 | 0.02 | 0.06 | 0.01 | 0.22 | 0.08 | 0.11 | 0.06 | 0.04 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.03 | 0.01 | 0.03 | 0.00 | 0.00 | 0.03 | 0.01 |
| BOC | ENSG00000144857 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.03 | 0.04 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.05 | 0.02 | 0.12 | 0.03 | 0.05 | 0.01 | 0.09 | 0.04 | 0.06 | 0.03 | 0.00 | 0.00 | 0.03 | 0.02 | 0.01 | 0.01 | 0.03 | 0.02 | 0.00 | 0.01 | 0.10 | 0.02 | 0.00 | 0.05 | 0.00 | 0.00 | 0.08 | 0.03 | 0.39 | 0.04 | 0.05 | 0.01 | 0.04 | 0.01 | 0.17 | 0.08 | 0.13 | 0.05 | 0.01 | 0.01 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.03 | 0.01 | 0.05 | 0.00 | 0.00 | 0.02 | 0.04 |
| UCN2 | ENSG00000145040 | 0.00 | 0.18 | 0.00 | 0.02 | 0.05 | 0.00 | 0.00 | 0.03 | 0.03 | 0.14 | 0.00 | 0.04 | 0.00 | 0.55 | 0.01 | 0.07 | 0.00 | 0.10 | 0.00 | 0.06 | 0.02 | 0.11 | 0.01 | 0.11 | 0.00 | 0.05 | 0.02 | 0.10 | 0.00 | 0.04 | 0.03 | 0.05 | 0.00 | 0.24 | 0.01 | 0.03 | 0.01 | 0.02 | 0.00 | 0.00 | 0.01 | 0.16 | 0.10 | 0.20 | 0.01 | 0.06 | 0.06 | 0.05 | 0.15 | 0.32 | 0.03 | 0.13 | 0.02 | 0.04 | 0.00 | 0.01 | 0.00 | 0.11 | 0.01 | 0.06 | 0.02 | 0.04 | 0.00 | 0.03 | 0.02 | 0.05 |
| VPRBP | ENSG00000145041 | 0.00 | 0.18 | 0.00 | 0.03 | 0.00 | 0.02 | 0.00 | 0.03 | 0.03 | 0.16 | 0.00 | 0.01 | 0.00 | 0.55 | 0.01 | 0.06 | 0.00 | 0.11 | 0.00 | 0.06 | 0.01 | 0.13 | 0.00 | 0.11 | 0.00 | 0.06 | 0.01 | 0.08 | 0.00 | 0.04 | 0.03 | 0.06 | 0.00 | 0.20 | 0.01 | 0.02 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.17 | 0.05 | 0.19 | 0.00 | 0.06 | 0.03 | 0.07 | 0.00 | 0.29 | 0.03 | 0.15 | 0.04 | 0.01 | 0.00 | 0.01 | 0.00 | 0.06 | 0.00 | 0.06 | 0.00 | 0.04 | 0.00 | 0.03 | 0.02 | 0.06 |
| MANF | ENSG00000145050 | 0.00 | 0.18 | 0.00 | 0.02 | 0.00 | 0.02 | 0.00 | 0.03 | 0.02 | 0.16 | 0.00 | 0.01 | 0.00 | 0.55 | 0.01 | 0.06 | 0.00 | 0.11 | 0.00 | 0.06 | 0.01 | 0.14 | 0.00 | 0.10 | 0.00 | 0.05 | 0.01 | 0.08 | 0.00 | 0.04 | 0.03 | 0.06 | 0.00 | 0.20 | 0.01 | 0.02 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.17 | 0.04 | 0.19 | 0.00 | 0.06 | 0.03 | 0.07 | 0.00 | 0.29 | 0.03 | 0.15 | 0.04 | 0.01 | 0.00 | 0.01 | 0.00 | 0.06 | 0.00 | 0.05 | 0.00 | 0.04 | 0.00 | 0.03 | 0.02 | 0.04 |
| SLIT2 | ENSG00000145147 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.05 | 0.04 | 0.04 | 0.00 | 0.00 | 0.00 | 0.01 | 0.06 | 0.03 | 0.01 | 0.07 | 0.02 | 0.05 | 0.03 | 0.05 | 0.03 | 0.02 | 0.01 | 0.02 | 0.03 | 0.03 | 0.00 | 0.01 | 0.02 | 0.04 | 0.00 | 0.01 | 0.05 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.05 | 0.16 | 0.11 | 0.01 | 0.04 | 0.04 | 0.08 | 0.21 | 0.10 | 0.11 | 0.05 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.05 | 0.00 | 0.05 | 0.02 |
| ECE2 | ENSG00000145194 | 0.05 | 0.00 | 0.03 | 0.01 | 0.00 | 0.01 | 0.03 | 0.03 | 0.17 | 0.00 | 0.00 | 0.00 | 0.00 | 0.08 | 0.15 | 0.05 | 1.85 | 0.00 | 0.66 | 0.00 | 0.69 | 0.02 | 0.23 | 0.00 | 0.04 | 0.00 | 0.06 | 0.03 | 0.03 | 0.01 | 0.11 | 0.02 | 0.12 | 0.01 | 0.10 | 0.00 | 0.00 | 0.10 | 0.00 | 0.00 | 0.19 | 0.02 | 1.12 | 0.02 | 0.62 | 0.00 | 0.34 | 0.01 | 0.76 | 0.09 | 0.11 | 0.10 | 0.22 | 0.00 | 0.00 | 0.01 | 0.06 | 0.00 | 0.06 | 0.00 | 0.20 | 0.02 | 0.00 | 0.00 | 0.03 | 0.05 |
| SLC26A1 | ENSG00000145217 | 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 |
| SLC10A4 | ENSG00000145248 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.02 | 0.05 | 0.03 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.09 | 0.02 | 0.17 | 0.03 | 0.05 | 0.02 | 0.10 | 0.04 | 0.03 | 0.04 | 0.01 | 0.01 | 0.00 | 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 | 0.13 | 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 |
| SLC10A6 | ENSG00000145283 | 0.01 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.03 | 0.02 | 0.17 | 0.06 | 0.00 | 0.00 | 0.00 | 0.07 | 0.02 | 0.04 | 0.08 | 0.05 | 0.04 | 0.03 | 0.05 | 0.07 | 0.03 | 0.07 | 0.01 | 0.02 | 0.00 | 0.01 | 0.00 | 0.01 | 0.01 | 0.10 | 0.00 | 0.03 | 0.09 | 0.02 | 0.02 | 0.02 | 0.00 | 0.00 | 0.04 | 0.04 | 0.05 | 0.23 | 0.05 | 0.03 | 0.03 | 0.03 | 0.02 | 0.09 | 0.07 | 0.07 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.05 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.04 |
| SNCA | ENSG00000145335 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.04 | 0.03 | 0.10 | 0.05 | 0.00 | 0.00 | 0.00 | 0.09 | 0.02 | 0.03 | 0.06 | 0.04 | 0.04 | 0.02 | 0.06 | 0.08 | 0.03 | 0.06 | 0.01 | 0.01 | 0.01 | 0.01 | 0.00 | 0.01 | 0.02 | 0.10 | 0.00 | 0.03 | 0.04 | 0.02 | 0.02 | 0.02 | 0.00 | 0.00 | 0.03 | 0.05 | 0.05 | 0.25 | 0.01 | 0.03 | 0.04 | 0.03 | 0.07 | 0.09 | 0.06 | 0.08 | 0.00 | 0.01 | 0.00 | 0.00 | 0.03 | 0.05 | 0.00 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.04 |
| FABP2 | ENSG00000145384 | 0.00 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.08 | 0.05 | 0.06 | 0.00 | 0.00 | 0.00 | 0.05 | 0.01 | 0.04 | 0.02 | 0.07 | 0.02 | 0.02 | 0.02 | 0.04 | 0.02 | 0.07 | 0.01 | 0.04 | 0.01 | 0.03 | 0.00 | 0.02 | 0.02 | 0.07 | 0.00 | 0.16 | 0.21 | 0.04 | 0.00 | 0.01 | 0.00 | 0.00 | 0.04 | 0.05 | 0.08 | 0.26 | 0.02 | 0.04 | 0.02 | 0.04 | 0.01 | 0.07 | 0.07 | 0.07 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.05 | 0.01 | 0.04 | 0.02 | 0.01 | 0.00 | 0.00 | 0.01 | 0.03 |
| CCNA2 | ENSG00000145386 | 0.00 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.07 | 0.05 | 0.07 | 0.00 | 0.00 | 0.00 | 0.04 | 0.02 | 0.04 | 0.02 | 0.06 | 0.03 | 0.02 | 0.01 | 0.04 | 0.02 | 0.06 | 0.01 | 0.04 | 0.01 | 0.02 | 0.00 | 0.02 | 0.05 | 0.07 | 0.00 | 0.11 | 0.11 | 0.05 | 0.00 | 0.01 | 0.00 | 0.00 | 0.05 | 0.04 | 0.05 | 0.24 | 0.01 | 0.04 | 0.01 | 0.04 | 0.07 | 0.07 | 0.07 | 0.07 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.05 | 0.01 | 0.04 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.03 |
| SFRP2 | ENSG00000145423 | 0.01 | 0.02 | 0.00 | 0.01 | 0.06 | 0.00 | 0.02 | 0.01 | 0.04 | 0.12 | 0.00 | 0.02 | 0.00 | 0.04 | 0.05 | 0.05 | 0.01 | 0.11 | 0.01 | 0.09 | 0.09 | 0.06 | 0.05 | 0.06 | 0.01 | 0.05 | 0.02 | 0.04 | 0.02 | 0.04 | 0.07 | 0.05 | 0.00 | 0.12 | 0.15 | 0.05 | 0.00 | 0.03 | 0.00 | 0.00 | 0.06 | 0.07 | 0.07 | 0.27 | 0.03 | 0.08 | 0.04 | 0.05 | 0.06 | 0.05 | 0.11 | 0.11 | 0.01 | 0.01 | 0.00 | 0.00 | 0.06 | 0.06 | 0.00 | 0.09 | 0.00 | 0.03 | 0.00 | 0.00 | 0.04 | 0.05 |
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