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 |
| CHRDL1 | ENSG00000101938 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.04 | 0.05 | 0.04 | 0.00 | 0.00 | 0.00 | 0.04 | 0.01 | 0.12 | 0.01 | 0.04 | 0.01 | 0.08 | 0.02 | 0.05 | 0.01 | 0.02 | 0.01 | 0.02 | 0.01 | 0.01 | 0.02 | 0.02 | 0.01 | 0.00 | 0.01 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.03 | 0.08 | 0.05 | 0.05 | 0.01 | 0.02 | 0.01 | 0.01 | 0.02 | 0.06 | 0.09 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.02 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.01 |
| SUV39H1 | ENSG00000101945 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.04 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.10 | 0.02 | 0.04 | 0.02 | 0.01 | 0.02 | 0.04 | 0.04 | 0.05 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.16 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.05 | 0.01 | 0.47 | 0.07 | 0.03 | 0.03 | 0.12 | 0.01 | 0.19 | 0.03 | 0.11 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.07 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.03 | 0.00 |
| F9 | ENSG00000101981 | 0.02 | 0.01 | 0.01 | 0.01 | 0.01 | 0.00 | 0.01 | 0.02 | 0.08 | 0.04 | 0.05 | 0.00 | 0.06 | 0.02 | 0.15 | 0.01 | 0.10 | 0.03 | 0.07 | 0.01 | 0.14 | 0.02 | 0.13 | 0.01 | 0.04 | 0.00 | 0.08 | 0.01 | 0.05 | 0.00 | 0.07 | 0.03 | 0.00 | 0.01 | 0.06 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.08 | 0.02 | 0.29 | 0.07 | 0.13 | 0.01 | 0.03 | 0.02 | 0.01 | 0.10 | 0.08 | 0.15 | 0.00 | 0.02 | 0.00 | 0.00 | 0.10 | 0.05 | 0.01 | 0.03 | 0.01 | 0.02 | 0.00 | 0.00 | 0.03 | 0.01 |
| ABCD1 | ENSG00000101986 | 0.03 | 0.01 | 0.02 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.12 | 0.04 | 0.06 | 0.00 | 0.06 | 0.01 | 0.23 | 0.01 | 0.19 | 0.02 | 0.14 | 0.01 | 0.26 | 0.01 | 0.17 | 0.02 | 0.05 | 0.01 | 0.10 | 0.01 | 0.07 | 0.00 | 0.12 | 0.03 | 0.10 | 0.01 | 0.11 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.11 | 0.03 | 0.45 | 0.09 | 0.22 | 0.02 | 0.11 | 0.03 | 0.09 | 0.07 | 0.24 | 0.07 | 0.01 | 0.02 | 0.00 | 0.00 | 0.15 | 0.07 | 0.02 | 0.03 | 0.03 | 0.02 | 0.05 | 0.00 | 0.06 | 0.01 |
| KCND1 | ENSG00000102057 | 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 |
| OPN1LW | ENSG00000102076 | 0.03 | 0.01 | 0.02 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.12 | 0.04 | 0.06 | 0.00 | 0.06 | 0.01 | 0.23 | 0.01 | 0.19 | 0.03 | 0.15 | 0.00 | 0.23 | 0.02 | 0.16 | 0.02 | 0.05 | 0.00 | 0.10 | 0.01 | 0.06 | 0.00 | 0.13 | 0.03 | 0.10 | 0.01 | 0.17 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.10 | 0.03 | 0.46 | 0.10 | 0.23 | 0.02 | 0.11 | 0.03 | 0.09 | 0.07 | 0.23 | 0.08 | 0.01 | 0.02 | 0.00 | 0.00 | 0.15 | 0.07 | 0.02 | 0.03 | 0.03 | 0.01 | 0.05 | 0.00 | 0.07 | 0.01 |
| FMR1 | ENSG00000102081 | 0.02 | 0.01 | 0.01 | 0.00 | 0.01 | 0.00 | 0.02 | 0.04 | 0.10 | 0.04 | 0.06 | 0.00 | 0.06 | 0.01 | 0.15 | 0.02 | 0.14 | 0.02 | 0.09 | 0.00 | 0.17 | 0.02 | 0.15 | 0.02 | 0.06 | 0.01 | 0.08 | 0.02 | 0.05 | 0.00 | 0.09 | 0.03 | 0.00 | 0.01 | 0.07 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.08 | 0.02 | 0.36 | 0.11 | 0.18 | 0.03 | 0.07 | 0.01 | 0.04 | 0.10 | 0.13 | 0.11 | 0.00 | 0.03 | 0.00 | 0.00 | 0.10 | 0.04 | 0.02 | 0.04 | 0.03 | 0.01 | 0.05 | 0.00 | 0.05 | 0.02 |
| PIM2 | ENSG00000102096 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.04 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.10 | 0.01 | 0.04 | 0.02 | 0.01 | 0.03 | 0.04 | 0.04 | 0.04 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.17 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.05 | 0.01 | 0.49 | 0.07 | 0.04 | 0.03 | 0.12 | 0.01 | 0.19 | 0.03 | 0.12 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.07 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.02 | 0.00 |
| SLC35A2 | ENSG00000102100 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.04 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.10 | 0.01 | 0.04 | 0.02 | 0.01 | 0.03 | 0.04 | 0.04 | 0.04 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.17 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.05 | 0.01 | 0.49 | 0.07 | 0.04 | 0.03 | 0.12 | 0.01 | 0.19 | 0.03 | 0.12 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.07 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.02 | 0.00 |
| RS1 | ENSG00000102104 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.06 | 0.01 | 0.04 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.04 | 0.11 | 0.04 | 0.03 | 0.02 | 0.09 | 0.05 | 0.03 | 0.02 | 0.00 | 0.01 | 0.10 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.00 | 0.01 | 0.10 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.06 | 0.03 | 0.10 | 0.14 | 0.06 | 0.02 | 0.04 | 0.01 | 0.10 | 0.07 | 0.14 | 0.04 | 0.07 | 0.01 | 0.00 | 0.00 | 0.04 | 0.04 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.04 | 0.02 |
| PCSK1N | ENSG00000102109 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.04 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.10 | 0.01 | 0.06 | 0.02 | 0.01 | 0.03 | 0.04 | 0.04 | 0.04 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.16 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.05 | 0.01 | 0.49 | 0.07 | 0.04 | 0.03 | 0.12 | 0.01 | 0.19 | 0.03 | 0.11 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.07 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.02 | 0.00 |
| SMS | ENSG00000102172 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.05 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.04 | 0.10 | 0.04 | 0.03 | 0.02 | 0.09 | 0.04 | 0.04 | 0.02 | 0.00 | 0.01 | 0.10 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.00 | 0.01 | 0.02 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.06 | 0.02 | 0.10 | 0.16 | 0.08 | 0.00 | 0.04 | 0.01 | 0.06 | 0.09 | 0.13 | 0.04 | 0.06 | 0.01 | 0.00 | 0.00 | 0.09 | 0.02 | 0.01 | 0.01 | 0.02 | 0.00 | 0.00 | 0.00 | 0.03 | 0.02 |
| GPR50 | ENSG00000102195 | 0.03 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.03 | 0.01 | 0.11 | 0.04 | 0.06 | 0.00 | 0.06 | 0.01 | 0.19 | 0.01 | 0.17 | 0.02 | 0.11 | 0.00 | 0.17 | 0.03 | 0.15 | 0.02 | 0.04 | 0.00 | 0.08 | 0.02 | 0.06 | 0.00 | 0.10 | 0.02 | 0.10 | 0.01 | 0.07 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.09 | 0.02 | 0.40 | 0.09 | 0.21 | 0.02 | 0.08 | 0.02 | 0.16 | 0.07 | 0.16 | 0.09 | 0.02 | 0.02 | 0.00 | 0.00 | 0.15 | 0.04 | 0.03 | 0.03 | 0.02 | 0.02 | 0.05 | 0.00 | 0.07 | 0.01 |
| JADE3 | ENSG00000102221 | 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 |
| CDK16 | ENSG00000102225 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.05 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.08 | 0.02 | 0.05 | 0.02 | 0.03 | 0.02 | 0.04 | 0.03 | 0.03 | 0.01 | 0.00 | 0.00 | 0.01 | 0.02 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.16 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.08 | 0.01 | 0.39 | 0.06 | 0.03 | 0.03 | 0.14 | 0.01 | 0.39 | 0.05 | 0.13 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.07 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.01 | 0.00 |
| CD40LG | ENSG00000102245 | 0.02 | 0.01 | 0.01 | 0.00 | 0.01 | 0.00 | 0.02 | 0.00 | 0.09 | 0.03 | 0.05 | 0.00 | 0.06 | 0.01 | 0.13 | 0.01 | 0.10 | 0.03 | 0.08 | 0.01 | 0.12 | 0.01 | 0.13 | 0.01 | 0.04 | 0.00 | 0.08 | 0.01 | 0.04 | 0.00 | 0.07 | 0.03 | 0.00 | 0.01 | 0.07 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.07 | 0.02 | 0.30 | 0.05 | 0.12 | 0.00 | 0.04 | 0.01 | 0.04 | 0.10 | 0.04 | 0.13 | 0.00 | 0.02 | 0.00 | 0.00 | 0.06 | 0.05 | 0.02 | 0.02 | 0.02 | 0.01 | 0.00 | 0.00 | 0.04 | 0.01 |
| TIMP1 | ENSG00000102265 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.06 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.07 | 0.02 | 0.05 | 0.02 | 0.04 | 0.02 | 0.04 | 0.03 | 0.04 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.16 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.07 | 0.01 | 0.36 | 0.06 | 0.03 | 0.03 | 0.13 | 0.01 | 0.34 | 0.03 | 0.12 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.07 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.01 | 0.00 |
| GABRE | ENSG00000102287 | 0.03 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.02 | 0.00 | 0.10 | 0.04 | 0.06 | 0.00 | 0.06 | 0.01 | 0.21 | 0.01 | 0.17 | 0.02 | 0.11 | 0.01 | 0.17 | 0.01 | 0.15 | 0.02 | 0.04 | 0.01 | 0.10 | 0.02 | 0.06 | 0.00 | 0.09 | 0.04 | 0.10 | 0.01 | 0.16 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.09 | 0.03 | 0.41 | 0.09 | 0.21 | 0.02 | 0.09 | 0.02 | 0.16 | 0.07 | 0.16 | 0.09 | 0.00 | 0.02 | 0.00 | 0.00 | 0.15 | 0.04 | 0.02 | 0.03 | 0.03 | 0.02 | 0.05 | 0.00 | 0.07 | 0.01 |
| PORCN | ENSG00000102312 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.04 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.09 | 0.03 | 0.05 | 0.02 | 0.02 | 0.02 | 0.04 | 0.04 | 0.04 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.17 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.06 | 0.01 | 0.44 | 0.07 | 0.03 | 0.03 | 0.11 | 0.01 | 0.19 | 0.03 | 0.11 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.07 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.02 | 0.00 |
| ITIH6 | ENSG00000102313 | 0.01 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.03 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.01 | 0.07 | 0.03 | 0.06 | 0.02 | 0.07 | 0.03 | 0.03 | 0.01 | 0.03 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.13 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.09 | 0.00 | 0.22 | 0.03 | 0.02 | 0.02 | 0.05 | 0.02 | 0.19 | 0.03 | 0.20 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.07 | 0.00 | 0.08 | 0.00 | 0.03 | 0.00 | 0.03 | 0.00 | 0.02 | 0.00 |
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