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 |
| MTNR1B | ENSG00000134640 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.03 | 0.03 | 0.02 | 0.09 | 0.05 | 0.00 | 0.00 | 0.06 | 0.08 | 0.08 | 0.03 | 0.07 | 0.08 | 0.10 | 0.09 | 0.16 | 0.04 | 0.05 | 0.03 | 0.02 | 0.01 | 0.01 | 0.02 | 0.00 | 0.01 | 0.02 | 0.05 | 0.00 | 0.10 | 0.00 | 0.02 | 0.00 | 0.04 | 0.00 | 0.00 | 0.10 | 0.12 | 0.32 | 0.09 | 0.13 | 0.07 | 0.05 | 0.03 | 0.08 | 0.16 | 0.08 | 0.12 | 0.04 | 0.07 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.08 | 0.08 |
| YARS | ENSG00000134684 | 0.00 | 0.04 | 0.00 | 0.06 | 0.00 | 0.00 | 0.02 | 0.01 | 0.03 | 0.07 | 0.00 | 0.01 | 0.11 | 0.07 | 0.06 | 0.04 | 0.05 | 0.05 | 0.06 | 0.04 | 0.07 | 0.05 | 0.07 | 0.05 | 0.02 | 0.08 | 0.01 | 0.11 | 0.01 | 0.03 | 0.03 | 0.18 | 0.06 | 0.61 | 0.06 | 0.05 | 0.02 | 0.08 | 0.00 | 0.00 | 0.05 | 0.09 | 0.36 | 0.22 | 0.06 | 0.03 | 0.08 | 0.06 | 0.09 | 0.04 | 0.14 | 0.05 | 0.03 | 0.03 | 0.02 | 0.00 | 0.00 | 0.10 | 0.00 | 0.01 | 0.05 | 0.04 | 0.00 | 0.07 | 0.05 | 0.05 |
| DAGLA | ENSG00000134780 | 0.01 | 0.00 | 0.00 | 0.01 | 0.09 | 0.00 | 0.01 | 0.01 | 0.11 | 0.01 | 0.00 | 0.00 | 0.14 | 0.00 | 0.06 | 0.01 | 0.05 | 0.02 | 0.11 | 0.02 | 0.13 | 0.02 | 0.04 | 0.03 | 0.01 | 0.01 | 0.02 | 0.02 | 0.00 | 0.02 | 0.07 | 0.02 | 0.15 | 0.07 | 0.08 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.12 | 0.06 | 0.12 | 0.04 | 0.06 | 0.00 | 0.06 | 0.01 | 0.26 | 0.18 | 0.07 | 0.04 | 0.00 | 0.08 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.05 | 0.04 |
| SLC43A3 | ENSG00000134802 | 0.00 | 0.00 | 0.00 | 0.01 | 0.09 | 0.00 | 0.00 | 0.01 | 0.13 | 0.02 | 0.00 | 0.00 | 0.06 | 0.02 | 0.05 | 0.03 | 0.09 | 0.02 | 0.12 | 0.01 | 0.14 | 0.04 | 0.01 | 0.05 | 0.01 | 0.01 | 0.01 | 0.03 | 0.00 | 0.02 | 0.04 | 0.02 | 0.00 | 0.12 | 0.04 | 0.00 | 0.02 | 0.03 | 0.00 | 0.00 | 0.11 | 0.06 | 0.11 | 0.05 | 0.07 | 0.02 | 0.06 | 0.02 | 0.32 | 0.09 | 0.09 | 0.05 | 0.01 | 0.03 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.01 | 0.01 | 0.03 | 0.00 | 0.00 | 0.04 | 0.02 |
| GIF | ENSG00000134812 | 0.01 | 0.00 | 0.00 | 0.01 | 0.09 | 0.00 | 0.02 | 0.01 | 0.15 | 0.02 | 0.00 | 0.00 | 0.09 | 0.01 | 0.04 | 0.02 | 0.07 | 0.03 | 0.11 | 0.03 | 0.10 | 0.04 | 0.02 | 0.04 | 0.01 | 0.01 | 0.03 | 0.02 | 0.00 | 0.02 | 0.02 | 0.03 | 0.04 | 0.07 | 0.06 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.09 | 0.08 | 0.11 | 0.05 | 0.05 | 0.01 | 0.05 | 0.01 | 0.16 | 0.13 | 0.04 | 0.04 | 0.00 | 0.05 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.07 | 0.04 |
| APLNR | ENSG00000134817 | 0.00 | 0.00 | 0.00 | 0.01 | 0.09 | 0.00 | 0.00 | 0.01 | 0.13 | 0.02 | 0.00 | 0.00 | 0.06 | 0.03 | 0.04 | 0.03 | 0.08 | 0.02 | 0.12 | 0.01 | 0.12 | 0.04 | 0.00 | 0.04 | 0.01 | 0.01 | 0.01 | 0.03 | 0.00 | 0.02 | 0.02 | 0.02 | 0.00 | 0.12 | 0.04 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.10 | 0.06 | 0.11 | 0.04 | 0.06 | 0.02 | 0.03 | 0.02 | 0.31 | 0.11 | 0.07 | 0.05 | 0.01 | 0.03 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.01 | 0.01 | 0.02 | 0.00 | 0.00 | 0.04 | 0.02 |
| C5AR2 | ENSG00000134830 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.05 | 0.07 | 0.04 | 0.00 | 0.02 | 0.00 | 0.09 | 0.01 | 0.08 | 0.04 | 0.11 | 0.02 | 0.02 | 0.05 | 0.04 | 0.04 | 0.03 | 0.01 | 0.03 | 0.03 | 0.04 | 0.02 | 0.05 | 0.03 | 0.04 | 0.00 | 0.10 | 0.13 | 0.03 | 0.00 | 0.03 | 0.00 | 0.00 | 0.04 | 0.06 | 0.03 | 0.33 | 0.05 | 0.08 | 0.03 | 0.06 | 0.06 | 0.19 | 0.02 | 0.21 | 0.00 | 0.04 | 0.01 | 0.00 | 0.07 | 0.03 | 0.00 | 0.14 | 0.01 | 0.14 | 0.00 | 0.00 | 0.02 | 0.03 |
| ERCC5 | ENSG00000134899 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.04 | 0.18 | 0.02 | 0.00 | 0.01 | 0.01 | 0.00 | 0.11 | 0.04 | 0.10 | 0.04 | 0.11 | 0.01 | 0.08 | 0.05 | 0.12 | 0.03 | 0.09 | 0.01 | 0.12 | 0.01 | 0.01 | 0.01 | 0.25 | 0.01 | 0.10 | 0.01 | 0.03 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.13 | 0.04 | 0.22 | 0.09 | 0.20 | 0.03 | 0.06 | 0.02 | 0.33 | 0.05 | 0.22 | 0.11 | 0.01 | 0.01 | 0.00 | 0.00 | 0.02 | 0.10 | 0.03 | 0.03 | 0.05 | 0.02 | 0.05 | 0.00 | 0.07 | 0.05 |
| TPP2 | ENSG00000134900 | 0.03 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.04 | 0.18 | 0.02 | 0.00 | 0.01 | 0.01 | 0.00 | 0.11 | 0.04 | 0.10 | 0.03 | 0.11 | 0.01 | 0.08 | 0.05 | 0.13 | 0.03 | 0.09 | 0.01 | 0.12 | 0.01 | 0.01 | 0.01 | 0.25 | 0.01 | 0.10 | 0.01 | 0.03 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.13 | 0.04 | 0.21 | 0.09 | 0.20 | 0.02 | 0.06 | 0.02 | 0.33 | 0.05 | 0.21 | 0.11 | 0.01 | 0.01 | 0.00 | 0.00 | 0.02 | 0.10 | 0.03 | 0.03 | 0.05 | 0.03 | 0.05 | 0.00 | 0.07 | 0.05 |
| ADAMTS8 | ENSG00000134917 | 0.00 | 0.01 | 0.00 | 0.05 | 0.00 | 0.05 | 0.03 | 0.04 | 0.03 | 0.11 | 0.00 | 0.00 | 0.14 | 0.06 | 0.06 | 0.09 | 0.05 | 0.13 | 0.04 | 0.14 | 0.09 | 0.15 | 0.05 | 0.07 | 0.01 | 0.01 | 0.01 | 0.02 | 0.02 | 0.02 | 0.03 | 0.09 | 0.00 | 0.23 | 0.02 | 0.06 | 0.00 | 0.05 | 0.00 | 0.00 | 0.05 | 0.20 | 0.27 | 0.18 | 0.04 | 0.31 | 0.06 | 0.07 | 0.16 | 0.19 | 0.04 | 0.24 | 0.00 | 0.28 | 0.04 | 0.00 | 0.13 | 0.00 | 0.05 | 0.01 | 0.01 | 0.01 | 0.00 | 0.07 | 0.01 | 0.26 |
| SLC37A2 | ENSG00000134955 | 0.00 | 0.01 | 0.00 | 0.05 | 0.00 | 0.02 | 0.02 | 0.06 | 0.03 | 0.10 | 0.00 | 0.00 | 0.11 | 0.04 | 0.06 | 0.09 | 0.04 | 0.11 | 0.04 | 0.14 | 0.04 | 0.16 | 0.05 | 0.08 | 0.01 | 0.01 | 0.01 | 0.03 | 0.01 | 0.02 | 0.00 | 0.09 | 0.00 | 0.19 | 0.00 | 0.06 | 0.00 | 0.05 | 0.00 | 0.00 | 0.02 | 0.22 | 0.19 | 0.18 | 0.04 | 0.31 | 0.03 | 0.08 | 0.05 | 0.17 | 0.01 | 0.23 | 0.00 | 0.28 | 0.03 | 0.00 | 0.13 | 0.02 | 0.07 | 0.01 | 0.01 | 0.01 | 0.00 | 0.07 | 0.00 | 0.26 |
| CTSL | ENSG00000135047 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.05 | 0.03 | 0.00 | 0.02 | 0.01 | 0.05 | 0.00 | 0.03 | 0.03 | 0.02 | 0.02 | 0.00 | 0.06 | 0.01 | 0.02 | 0.05 | 0.02 | 0.01 | 0.02 | 0.02 | 0.00 | 0.00 | 0.02 | 0.02 | 0.00 | 0.15 | 0.02 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.03 | 0.03 | 0.05 | 0.14 | 0.00 | 0.02 | 0.04 | 0.03 | 0.03 | 0.15 | 0.10 | 0.00 | 0.04 | 0.02 | 0.00 | 0.02 | 0.05 | 0.02 | 0.00 | 0.01 | 0.01 | 0.02 | 0.00 | 0.00 | 0.01 | 0.02 |
| CSN2 | ENSG00000135222 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.03 | 0.12 | 0.02 | 0.00 | 0.00 | 0.00 | 0.07 | 0.07 | 0.03 | 0.21 | 0.01 | 0.08 | 0.02 | 0.13 | 0.02 | 0.05 | 0.03 | 0.01 | 0.01 | 0.04 | 0.01 | 0.00 | 0.01 | 0.02 | 0.07 | 0.00 | 0.03 | 0.03 | 0.00 | 0.02 | 0.02 | 0.00 | 0.00 | 0.09 | 0.02 | 0.24 | 0.08 | 0.04 | 0.04 | 0.04 | 0.01 | 0.06 | 0.05 | 0.05 | 0.05 | 0.08 | 0.01 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.03 | 0.00 | 0.02 | 0.00 | 0.00 | 0.02 | 0.03 |
| UGT2B28 | ENSG00000135226 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.04 | 0.12 | 0.03 | 0.00 | 0.00 | 0.00 | 0.06 | 0.05 | 0.03 | 0.23 | 0.01 | 0.08 | 0.02 | 0.13 | 0.01 | 0.04 | 0.02 | 0.01 | 0.01 | 0.03 | 0.01 | 0.00 | 0.01 | 0.03 | 0.06 | 0.00 | 0.03 | 0.03 | 0.00 | 0.02 | 0.02 | 0.00 | 0.00 | 0.09 | 0.02 | 0.27 | 0.08 | 0.04 | 0.04 | 0.04 | 0.01 | 0.06 | 0.05 | 0.07 | 0.06 | 0.09 | 0.01 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.02 | 0.00 | 0.02 | 0.00 | 0.00 | 0.02 | 0.04 |
| HILPDA | ENSG00000135245 | 0.01 | 0.01 | 0.08 | 0.00 | 0.01 | 0.00 | 0.02 | 0.05 | 0.04 | 0.04 | 0.00 | 0.01 | 0.04 | 0.05 | 0.07 | 0.02 | 0.07 | 0.07 | 0.02 | 0.13 | 0.03 | 0.19 | 0.04 | 0.06 | 0.03 | 0.01 | 0.06 | 0.02 | 0.01 | 0.04 | 0.05 | 0.05 | 0.00 | 0.02 | 0.01 | 0.06 | 0.00 | 0.02 | 0.00 | 0.00 | 0.10 | 0.04 | 0.36 | 0.04 | 0.03 | 0.07 | 0.07 | 0.05 | 0.08 | 0.14 | 0.13 | 0.02 | 0.03 | 0.03 | 0.00 | 0.06 | 0.02 | 0.11 | 0.11 | 0.00 | 0.06 | 0.00 | 0.00 | 0.00 | 0.19 | 0.02 |
| HTR1B | ENSG00000135312 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.17 | 0.02 | 0.07 | 0.00 | 0.00 | 0.01 | 0.03 | 0.03 | 0.05 | 0.08 | 0.04 | 0.03 | 0.04 | 0.04 | 0.07 | 0.04 | 0.06 | 0.00 | 0.02 | 0.02 | 0.02 | 0.01 | 0.02 | 0.03 | 0.03 | 0.00 | 0.19 | 0.06 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.08 | 0.14 | 0.11 | 0.03 | 0.02 | 0.02 | 0.01 | 0.14 | 0.08 | 0.01 | 0.15 | 0.03 | 0.00 | 0.00 | 0.00 | 0.01 | 0.20 | 0.00 | 0.00 | 0.00 | 0.04 | 0.00 | 0.05 | 0.02 | 0.04 |
| CD63 | ENSG00000135404 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.04 | 0.02 | 0.00 | 0.00 | 0.02 | 0.02 | 0.08 | 0.01 | 0.04 | 0.02 | 0.01 | 0.02 | 0.06 | 0.03 | 0.10 | 0.02 | 0.02 | 0.00 | 0.02 | 0.01 | 0.02 | 0.01 | 0.03 | 0.00 | 0.00 | 0.01 | 0.18 | 0.00 | 0.06 | 0.00 | 0.00 | 0.00 | 0.04 | 0.05 | 0.19 | 0.04 | 0.03 | 0.00 | 0.08 | 0.01 | 0.14 | 0.07 | 0.29 | 0.07 | 0.01 | 0.00 | 0.00 | 0.00 | 0.12 | 0.00 | 0.01 | 0.03 | 0.04 | 0.04 | 0.00 | 0.00 | 0.06 | 0.03 |
| LACRT | ENSG00000135413 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.09 | 0.02 | 0.00 | 0.00 | 0.02 | 0.02 | 0.07 | 0.01 | 0.04 | 0.02 | 0.01 | 0.02 | 0.05 | 0.03 | 0.06 | 0.02 | 0.02 | 0.00 | 0.02 | 0.01 | 0.00 | 0.02 | 0.02 | 0.01 | 0.17 | 0.01 | 0.30 | 0.00 | 0.06 | 0.00 | 0.00 | 0.00 | 0.04 | 0.05 | 0.16 | 0.04 | 0.06 | 0.00 | 0.04 | 0.01 | 0.14 | 0.09 | 0.14 | 0.08 | 0.01 | 0.00 | 0.00 | 0.00 | 0.12 | 0.00 | 0.01 | 0.04 | 0.03 | 0.05 | 0.08 | 0.00 | 0.03 | 0.05 |
| RDH5 | ENSG00000135437 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.04 | 0.02 | 0.00 | 0.00 | 0.02 | 0.02 | 0.08 | 0.01 | 0.04 | 0.02 | 0.01 | 0.02 | 0.06 | 0.03 | 0.10 | 0.02 | 0.02 | 0.00 | 0.02 | 0.01 | 0.02 | 0.01 | 0.03 | 0.00 | 0.00 | 0.01 | 0.18 | 0.00 | 0.06 | 0.00 | 0.00 | 0.00 | 0.04 | 0.05 | 0.19 | 0.04 | 0.03 | 0.00 | 0.08 | 0.01 | 0.14 | 0.07 | 0.29 | 0.07 | 0.01 | 0.00 | 0.00 | 0.00 | 0.12 | 0.00 | 0.01 | 0.03 | 0.04 | 0.04 | 0.00 | 0.00 | 0.06 | 0.03 |
| CDK4 | ENSG00000135446 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.11 | 0.03 | 0.00 | 0.00 | 0.02 | 0.02 | 0.33 | 0.00 | 0.08 | 0.01 | 0.04 | 0.02 | 0.11 | 0.04 | 0.18 | 0.01 | 0.01 | 0.00 | 0.04 | 0.01 | 0.04 | 0.02 | 0.09 | 0.01 | 0.31 | 0.01 | 0.44 | 0.02 | 0.07 | 0.00 | 0.00 | 0.00 | 0.14 | 0.03 | 0.16 | 0.05 | 0.03 | 0.00 | 0.02 | 0.01 | 0.10 | 0.05 | 1.74 | 0.07 | 0.00 | 0.00 | 0.00 | 0.00 | 0.12 | 0.00 | 0.38 | 0.01 | 1.24 | 0.02 | 0.00 | 0.00 | 0.28 | 0.03 |
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