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 |
| CDC25B | ENSG00000101224 | 0.01 | 0.00 | 0.01 | 0.00 | 0.05 | 0.00 | 0.01 | 0.03 | 0.04 | 0.02 | 0.00 | 0.00 | 0.00 | 0.05 | 0.03 | 0.04 | 0.14 | 0.01 | 0.03 | 0.03 | 0.07 | 0.03 | 0.06 | 0.01 | 0.06 | 0.04 | 0.05 | 0.08 | 0.00 | 0.03 | 0.05 | 0.01 | 0.00 | 0.03 | 0.01 | 0.08 | 0.00 | 0.01 | 0.00 | 0.00 | 0.07 | 0.05 | 0.29 | 0.07 | 0.04 | 0.01 | 0.10 | 0.03 | 0.09 | 0.06 | 0.08 | 0.07 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.01 | 0.01 | 0.02 | 0.00 | 0.02 | 0.02 |
| CSNK2A1 | ENSG00000101266 | 0.01 | 0.00 | 0.01 | 0.00 | 0.03 | 0.01 | 0.01 | 0.02 | 0.04 | 0.02 | 0.00 | 0.00 | 0.00 | 0.05 | 0.04 | 0.05 | 0.14 | 0.03 | 0.03 | 0.03 | 0.10 | 0.03 | 0.05 | 0.02 | 0.04 | 0.05 | 0.09 | 0.09 | 0.03 | 0.03 | 0.05 | 0.01 | 0.04 | 0.03 | 0.00 | 0.10 | 0.00 | 0.02 | 0.00 | 0.00 | 0.05 | 0.08 | 0.34 | 0.10 | 0.03 | 0.03 | 0.07 | 0.03 | 0.11 | 0.10 | 0.08 | 0.09 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.01 | 0.02 | 0.02 | 0.00 | 0.04 | 0.04 |
| SLC52A3 | ENSG00000101276 | 0.01 | 0.00 | 0.01 | 0.00 | 0.03 | 0.01 | 0.00 | 0.02 | 0.04 | 0.02 | 0.00 | 0.00 | 0.00 | 0.05 | 0.04 | 0.05 | 0.13 | 0.02 | 0.03 | 0.03 | 0.09 | 0.03 | 0.05 | 0.02 | 0.04 | 0.05 | 0.09 | 0.09 | 0.03 | 0.03 | 0.05 | 0.01 | 0.04 | 0.03 | 0.00 | 0.10 | 0.00 | 0.02 | 0.00 | 0.00 | 0.05 | 0.08 | 0.33 | 0.10 | 0.03 | 0.03 | 0.07 | 0.03 | 0.14 | 0.17 | 0.07 | 0.09 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.01 | 0.01 | 0.02 | 0.00 | 0.03 | 0.03 |
| ANGPT4 | ENSG00000101280 | 0.01 | 0.00 | 0.01 | 0.00 | 0.03 | 0.01 | 0.01 | 0.02 | 0.04 | 0.02 | 0.00 | 0.00 | 0.00 | 0.05 | 0.04 | 0.05 | 0.13 | 0.02 | 0.03 | 0.03 | 0.09 | 0.03 | 0.04 | 0.02 | 0.04 | 0.05 | 0.09 | 0.08 | 0.03 | 0.03 | 0.04 | 0.01 | 0.04 | 0.03 | 0.02 | 0.10 | 0.00 | 0.02 | 0.00 | 0.00 | 0.05 | 0.07 | 0.32 | 0.10 | 0.03 | 0.03 | 0.07 | 0.03 | 0.14 | 0.10 | 0.07 | 0.09 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.01 | 0.01 | 0.02 | 0.00 | 0.03 | 0.03 |
| RSPO4 | ENSG00000101282 | 0.01 | 0.00 | 0.01 | 0.00 | 0.03 | 0.01 | 0.01 | 0.02 | 0.04 | 0.02 | 0.00 | 0.00 | 0.00 | 0.05 | 0.04 | 0.05 | 0.13 | 0.02 | 0.03 | 0.03 | 0.09 | 0.03 | 0.05 | 0.02 | 0.03 | 0.05 | 0.09 | 0.09 | 0.03 | 0.03 | 0.04 | 0.01 | 0.04 | 0.03 | 0.02 | 0.10 | 0.00 | 0.02 | 0.00 | 0.00 | 0.04 | 0.07 | 0.33 | 0.10 | 0.03 | 0.03 | 0.07 | 0.03 | 0.14 | 0.08 | 0.07 | 0.09 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.01 | 0.01 | 0.02 | 0.00 | 0.03 | 0.03 |
| PROKR2 | ENSG00000101292 | 0.01 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.01 | 0.03 | 0.03 | 0.03 | 0.00 | 0.00 | 0.00 | 0.03 | 0.03 | 0.04 | 0.12 | 0.01 | 0.05 | 0.02 | 0.07 | 0.03 | 0.05 | 0.01 | 0.06 | 0.04 | 0.05 | 0.09 | 0.00 | 0.02 | 0.03 | 0.01 | 0.00 | 0.01 | 0.02 | 0.08 | 0.01 | 0.01 | 0.00 | 0.00 | 0.05 | 0.04 | 0.27 | 0.07 | 0.07 | 0.01 | 0.06 | 0.02 | 0.06 | 0.06 | 0.05 | 0.07 | 0.00 | 0.02 | 0.00 | 0.00 | 0.06 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.02 | 0.00 | 0.03 | 0.02 |
| SIRPB1 | ENSG00000101307 | 0.01 | 0.00 | 0.01 | 0.00 | 0.03 | 0.01 | 0.00 | 0.02 | 0.03 | 0.02 | 0.00 | 0.00 | 0.00 | 0.03 | 0.04 | 0.05 | 0.12 | 0.02 | 0.02 | 0.02 | 0.07 | 0.03 | 0.05 | 0.01 | 0.05 | 0.05 | 0.08 | 0.08 | 0.02 | 0.03 | 0.04 | 0.01 | 0.04 | 0.03 | 0.00 | 0.09 | 0.00 | 0.02 | 0.00 | 0.00 | 0.04 | 0.06 | 0.30 | 0.09 | 0.03 | 0.03 | 0.07 | 0.03 | 0.14 | 0.07 | 0.07 | 0.08 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.01 | 0.02 | 0.02 | 0.00 | 0.02 | 0.03 |
| HAO1 | ENSG00000101323 | 0.00 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.02 | 0.02 | 0.03 | 0.03 | 0.00 | 0.00 | 0.00 | 0.03 | 0.04 | 0.03 | 0.15 | 0.01 | 0.05 | 0.02 | 0.07 | 0.02 | 0.04 | 0.01 | 0.04 | 0.05 | 0.05 | 0.07 | 0.00 | 0.02 | 0.04 | 0.00 | 0.00 | 0.03 | 0.03 | 0.08 | 0.00 | 0.01 | 0.00 | 0.00 | 0.04 | 0.05 | 0.23 | 0.07 | 0.06 | 0.01 | 0.06 | 0.01 | 0.04 | 0.12 | 0.06 | 0.05 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.02 |
| PDYN | ENSG00000101327 | 0.01 | 0.00 | 0.01 | 0.00 | 0.03 | 0.01 | 0.00 | 0.02 | 0.03 | 0.02 | 0.00 | 0.00 | 0.00 | 0.03 | 0.04 | 0.05 | 0.13 | 0.01 | 0.03 | 0.02 | 0.08 | 0.03 | 0.04 | 0.02 | 0.04 | 0.04 | 0.06 | 0.10 | 0.01 | 0.03 | 0.04 | 0.01 | 0.04 | 0.03 | 0.01 | 0.09 | 0.00 | 0.02 | 0.00 | 0.00 | 0.04 | 0.06 | 0.32 | 0.09 | 0.02 | 0.03 | 0.07 | 0.03 | 0.11 | 0.07 | 0.07 | 0.07 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.01 | 0.02 | 0.02 | 0.00 | 0.02 | 0.03 |
| OXT | ENSG00000101405 | 0.01 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.02 | 0.04 | 0.02 | 0.00 | 0.00 | 0.00 | 0.03 | 0.03 | 0.04 | 0.13 | 0.01 | 0.03 | 0.03 | 0.07 | 0.03 | 0.04 | 0.01 | 0.06 | 0.04 | 0.06 | 0.09 | 0.01 | 0.03 | 0.04 | 0.01 | 0.00 | 0.03 | 0.00 | 0.09 | 0.00 | 0.01 | 0.00 | 0.00 | 0.05 | 0.05 | 0.33 | 0.07 | 0.04 | 0.02 | 0.09 | 0.03 | 0.09 | 0.07 | 0.07 | 0.06 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.01 | 0.01 | 0.02 | 0.00 | 0.02 | 0.02 |
| SLC32A1 | ENSG00000101438 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.03 | 0.07 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.04 | 0.04 | 0.09 | 0.01 | 0.02 | 0.01 | 0.06 | 0.01 | 0.08 | 0.00 | 0.07 | 0.00 | 0.17 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.00 | 0.04 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.10 | 0.02 | 0.07 | 0.08 | 0.05 | 0.02 | 0.03 | 0.01 | 0.06 | 0.00 | 0.11 | 0.05 | 0.00 | 0.01 | 0.00 | 0.03 | 0.04 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.04 | 0.00 |
| ASIP | ENSG00000101440 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.02 | 0.02 | 0.21 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.08 | 0.02 | 0.17 | 0.01 | 0.22 | 0.00 | 0.10 | 0.00 | 0.05 | 0.01 | 0.11 | 0.00 | 0.21 | 0.00 | 0.00 | 0.01 | 0.05 | 0.00 | 0.00 | 0.01 | 0.14 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.07 | 0.02 | 0.18 | 0.03 | 0.15 | 0.00 | 0.11 | 0.01 | 0.35 | 0.00 | 0.13 | 0.03 | 0.01 | 0.01 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.06 | 0.01 |
| CST4 | ENSG00000101441 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.02 | 0.05 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.08 | 0.02 | 0.05 | 0.03 | 0.04 | 0.02 | 0.08 | 0.03 | 0.06 | 0.01 | 0.05 | 0.01 | 0.03 | 0.02 | 0.04 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.04 | 0.03 | 0.08 | 0.04 | 0.04 | 0.02 | 0.03 | 0.01 | 0.05 | 0.00 | 0.10 | 0.01 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.00 | 0.03 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.02 |
| WFDC2 | ENSG00000101443 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.01 | 0.18 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.05 | 0.08 | 0.01 | 0.01 | 0.01 | 0.09 | 0.00 | 0.19 | 0.00 | 0.19 | 0.00 | 0.12 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.14 | 0.02 | 0.22 | 0.05 | 0.02 | 0.04 | 0.10 | 0.01 | 0.29 | 0.00 | 0.11 | 0.03 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.05 | 0.01 |
| SPINT3 | ENSG00000101446 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.16 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.05 | 0.07 | 0.01 | 0.01 | 0.01 | 0.09 | 0.00 | 0.17 | 0.00 | 0.19 | 0.00 | 0.12 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.14 | 0.02 | 0.22 | 0.05 | 0.02 | 0.04 | 0.10 | 0.01 | 0.29 | 0.00 | 0.11 | 0.03 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.06 | 0.01 |
| ATG4A | ENSG00000101844 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.03 | 0.03 | 0.00 | 0.00 | 0.04 | 0.03 | 0.01 | 0.15 | 0.01 | 0.03 | 0.01 | 0.10 | 0.02 | 0.05 | 0.02 | 0.02 | 0.01 | 0.02 | 0.01 | 0.00 | 0.01 | 0.03 | 0.01 | 0.00 | 0.01 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.03 | 0.08 | 0.06 | 0.04 | 0.00 | 0.02 | 0.02 | 0.04 | 0.02 | 0.07 | 0.11 | 0.00 | 0.01 | 0.00 | 0.00 | 0.04 | 0.02 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 |
| STS | ENSG00000101846 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.04 | 0.04 | 0.00 | 0.07 | 0.05 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.06 | 0.10 | 0.07 | 0.03 | 0.02 | 0.06 | 0.07 | 0.06 | 0.04 | 0.01 | 0.02 | 0.11 | 0.03 | 0.00 | 0.01 | 0.01 | 0.02 | 0.02 | 0.01 | 0.09 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.05 | 0.04 | 0.15 | 0.20 | 0.07 | 0.02 | 0.05 | 0.04 | 0.09 | 0.09 | 0.11 | 0.10 | 0.04 | 0.02 | 0.00 | 0.00 | 0.00 | 0.04 | 0.02 | 0.02 | 0.01 | 0.01 | 0.00 | 0.00 | 0.04 | 0.03 |
| GPR143 | ENSG00000101850 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.04 | 0.05 | 0.00 | 0.07 | 0.06 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.08 | 0.09 | 0.08 | 0.02 | 0.06 | 0.05 | 0.07 | 0.06 | 0.04 | 0.01 | 0.02 | 0.13 | 0.04 | 0.00 | 0.01 | 0.02 | 0.02 | 0.00 | 0.01 | 0.07 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.05 | 0.03 | 0.12 | 0.19 | 0.07 | 0.02 | 0.04 | 0.02 | 0.09 | 0.16 | 0.10 | 0.07 | 0.05 | 0.01 | 0.00 | 0.00 | 0.00 | 0.04 | 0.01 | 0.02 | 0.01 | 0.02 | 0.00 | 0.00 | 0.04 | 0.03 |
| PRPS2 | ENSG00000101911 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.05 | 0.05 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.05 | 0.09 | 0.06 | 0.02 | 0.02 | 0.06 | 0.05 | 0.06 | 0.02 | 0.01 | 0.01 | 0.08 | 0.02 | 0.01 | 0.01 | 0.02 | 0.02 | 0.00 | 0.01 | 0.07 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.05 | 0.03 | 0.13 | 0.18 | 0.06 | 0.00 | 0.04 | 0.03 | 0.06 | 0.12 | 0.09 | 0.05 | 0.06 | 0.02 | 0.00 | 0.00 | 0.00 | 0.04 | 0.02 | 0.01 | 0.02 | 0.03 | 0.00 | 0.00 | 0.04 | 0.02 |
| TLR8 | ENSG00000101916 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.05 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.05 | 0.09 | 0.05 | 0.02 | 0.02 | 0.07 | 0.03 | 0.08 | 0.02 | 0.01 | 0.01 | 0.08 | 0.02 | 0.01 | 0.01 | 0.03 | 0.02 | 0.00 | 0.01 | 0.07 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.05 | 0.03 | 0.14 | 0.18 | 0.06 | 0.00 | 0.04 | 0.02 | 0.06 | 0.12 | 0.09 | 0.05 | 0.06 | 0.01 | 0.00 | 0.00 | 0.00 | 0.04 | 0.02 | 0.01 | 0.02 | 0.00 | 0.00 | 0.00 | 0.04 | 0.02 |
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