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 |
| SLC19A2 | ENSG00000117479 | 0.03 | 0.00 | 0.01 | 0.01 | 0.00 | 0.03 | 0.01 | 0.04 | 0.46 | 0.01 | 0.02 | 0.02 | 0.10 | 0.03 | 0.14 | 0.01 | 0.24 | 0.01 | 0.04 | 0.00 | 0.22 | 0.01 | 0.12 | 0.01 | 0.03 | 0.00 | 0.11 | 0.00 | 0.06 | 0.00 | 0.22 | 0.00 | 0.22 | 0.01 | 0.00 | 0.04 | 0.04 | 0.00 | 0.00 | 0.00 | 0.19 | 0.02 | 0.32 | 0.02 | 0.11 | 0.01 | 0.10 | 0.00 | 0.29 | 0.00 | 0.39 | 0.05 | 0.10 | 0.00 | 0.00 | 0.00 | 0.36 | 0.04 | 0.01 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.14 | 0.01 |
| F3 | ENSG00000117525 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.08 | 0.05 | 0.07 | 0.00 | 0.00 | 0.00 | 0.39 | 0.02 | 0.11 | 0.04 | 0.07 | 0.01 | 0.07 | 0.01 | 0.09 | 0.03 | 0.07 | 0.00 | 0.06 | 0.03 | 0.06 | 0.00 | 0.02 | 0.01 | 0.02 | 0.04 | 0.15 | 0.02 | 0.04 | 0.00 | 0.22 | 0.00 | 0.00 | 0.05 | 0.11 | 0.13 | 0.16 | 0.01 | 0.06 | 0.04 | 0.03 | 0.06 | 0.06 | 0.09 | 0.09 | 0.03 | 0.08 | 0.01 | 0.01 | 0.00 | 0.03 | 0.01 | 0.01 | 0.01 | 0.05 | 0.00 | 0.05 | 0.03 | 0.12 |
| ABCD3 | ENSG00000117528 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.08 | 0.06 | 0.07 | 0.00 | 0.00 | 0.00 | 0.39 | 0.02 | 0.11 | 0.04 | 0.07 | 0.01 | 0.07 | 0.02 | 0.09 | 0.03 | 0.07 | 0.00 | 0.06 | 0.02 | 0.06 | 0.00 | 0.02 | 0.02 | 0.02 | 0.04 | 0.16 | 0.02 | 0.04 | 0.00 | 0.23 | 0.00 | 0.00 | 0.05 | 0.11 | 0.14 | 0.16 | 0.00 | 0.06 | 0.04 | 0.03 | 0.06 | 0.06 | 0.09 | 0.09 | 0.03 | 0.08 | 0.01 | 0.01 | 0.00 | 0.03 | 0.01 | 0.01 | 0.01 | 0.06 | 0.00 | 0.05 | 0.03 | 0.12 |
| TNFSF4 | ENSG00000117586 | 0.03 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.04 | 0.36 | 0.02 | 0.02 | 0.00 | 0.10 | 0.03 | 0.13 | 0.00 | 0.23 | 0.01 | 0.06 | 0.00 | 0.22 | 0.02 | 0.11 | 0.01 | 0.04 | 0.00 | 0.12 | 0.00 | 0.05 | 0.00 | 0.22 | 0.00 | 0.17 | 0.01 | 0.00 | 0.04 | 0.05 | 0.00 | 0.00 | 0.00 | 0.17 | 0.01 | 0.34 | 0.03 | 0.13 | 0.00 | 0.11 | 0.00 | 0.29 | 0.00 | 0.47 | 0.04 | 0.10 | 0.00 | 0.00 | 0.00 | 0.30 | 0.00 | 0.01 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.15 | 0.01 |
| NEK2 | ENSG00000117650 | 0.01 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.05 | 0.07 | 0.06 | 0.01 | 0.00 | 0.07 | 0.03 | 0.10 | 0.01 | 0.09 | 0.01 | 0.05 | 0.00 | 0.17 | 0.05 | 0.07 | 0.01 | 0.04 | 0.01 | 0.07 | 0.03 | 0.01 | 0.00 | 0.15 | 0.02 | 0.16 | 0.02 | 0.04 | 0.03 | 0.01 | 0.00 | 0.00 | 0.00 | 0.21 | 0.02 | 0.16 | 0.17 | 0.06 | 0.01 | 0.08 | 0.02 | 0.13 | 0.04 | 0.04 | 0.20 | 0.02 | 0.03 | 0.01 | 0.00 | 0.16 | 0.04 | 0.00 | 0.01 | 0.02 | 0.04 | 0.09 | 0.00 | 0.12 | 0.03 |
| NENF | ENSG00000117691 | 0.01 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.05 | 0.07 | 0.06 | 0.01 | 0.00 | 0.05 | 0.04 | 0.09 | 0.02 | 0.09 | 0.01 | 0.05 | 0.00 | 0.17 | 0.04 | 0.07 | 0.02 | 0.04 | 0.01 | 0.07 | 0.03 | 0.00 | 0.00 | 0.14 | 0.02 | 0.16 | 0.02 | 0.01 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.20 | 0.02 | 0.16 | 0.17 | 0.05 | 0.02 | 0.07 | 0.02 | 0.13 | 0.04 | 0.03 | 0.21 | 0.02 | 0.03 | 0.01 | 0.00 | 0.16 | 0.04 | 0.00 | 0.02 | 0.01 | 0.06 | 0.09 | 0.00 | 0.12 | 0.03 |
| TXNDC12 | ENSG00000117862 | 0.00 | 0.01 | 0.02 | 0.02 | 0.00 | 0.00 | 0.00 | 0.06 | 0.08 | 0.03 | 0.00 | 0.00 | 0.06 | 0.04 | 0.08 | 0.04 | 0.05 | 0.03 | 0.04 | 0.03 | 0.03 | 0.03 | 0.02 | 0.04 | 0.01 | 0.04 | 0.02 | 0.03 | 0.01 | 0.01 | 0.02 | 0.06 | 0.00 | 0.25 | 0.02 | 0.03 | 0.00 | 0.16 | 0.00 | 0.00 | 0.06 | 0.05 | 0.30 | 0.10 | 0.07 | 0.01 | 0.05 | 0.02 | 0.03 | 0.03 | 0.24 | 0.02 | 0.08 | 0.04 | 0.02 | 0.00 | 0.00 | 0.03 | 0.00 | 0.01 | 0.02 | 0.03 | 0.00 | 0.07 | 0.04 | 0.03 |
| MMP8 | ENSG00000118113 | 0.02 | 0.01 | 0.00 | 0.05 | 0.03 | 0.03 | 0.02 | 0.04 | 0.28 | 0.06 | 0.00 | 0.00 | 0.06 | 0.06 | 0.11 | 0.05 | 0.11 | 0.07 | 0.39 | 0.10 | 0.13 | 0.08 | 0.09 | 0.05 | 0.04 | 0.01 | 0.02 | 0.04 | 0.05 | 0.01 | 0.05 | 0.06 | 0.00 | 0.10 | 0.01 | 0.05 | 0.00 | 0.04 | 0.00 | 0.00 | 0.06 | 0.19 | 0.35 | 0.13 | 0.73 | 0.11 | 0.07 | 0.04 | 0.10 | 0.17 | 0.24 | 0.15 | 0.01 | 0.08 | 0.02 | 0.00 | 0.04 | 0.01 | 0.01 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.12 | 0.13 |
| APOA1 | ENSG00000118137 | 0.00 | 0.01 | 0.00 | 0.06 | 0.02 | 0.02 | 0.01 | 0.09 | 0.03 | 0.11 | 0.00 | 0.00 | 0.02 | 0.06 | 0.04 | 0.08 | 0.04 | 0.10 | 0.04 | 0.16 | 0.07 | 0.13 | 0.06 | 0.08 | 0.01 | 0.02 | 0.00 | 0.03 | 0.01 | 0.01 | 0.02 | 0.09 | 0.00 | 0.17 | 0.00 | 0.05 | 0.00 | 0.06 | 0.00 | 0.00 | 0.02 | 0.24 | 0.14 | 0.17 | 0.04 | 0.29 | 0.03 | 0.05 | 0.11 | 0.18 | 0.02 | 0.21 | 0.01 | 0.14 | 0.02 | 0.00 | 0.11 | 0.01 | 0.04 | 0.01 | 0.03 | 0.01 | 0.00 | 0.07 | 0.00 | 0.27 |
| TTR | ENSG00000118271 | 0.00 | 0.00 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.02 | 0.07 | 0.01 | 0.00 | 0.00 | 0.02 | 0.03 | 0.09 | 0.02 | 0.18 | 0.01 | 0.08 | 0.02 | 0.15 | 0.05 | 0.09 | 0.06 | 0.01 | 0.02 | 0.03 | 0.01 | 0.06 | 0.05 | 0.02 | 0.01 | 0.00 | 0.01 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.02 | 0.30 | 0.07 | 0.02 | 0.00 | 0.05 | 0.01 | 0.07 | 0.00 | 0.13 | 0.04 | 0.02 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 |
| ATP10B | ENSG00000118322 | 0.31 | 0.00 | 0.04 | 0.01 | 0.00 | 0.00 | 0.04 | 0.01 | 0.01 | 0.08 | 0.02 | 0.00 | 0.02 | 0.07 | 0.06 | 0.04 | 0.02 | 0.05 | 0.01 | 0.05 | 0.04 | 0.05 | 0.03 | 0.04 | 0.01 | 0.02 | 0.04 | 0.03 | 0.02 | 0.01 | 0.11 | 0.03 | 0.09 | 0.01 | 0.23 | 0.02 | 0.00 | 0.03 | 0.01 | 0.00 | 0.05 | 0.04 | 0.17 | 0.15 | 0.03 | 0.02 | 0.02 | 0.02 | 0.15 | 0.01 | 0.13 | 0.08 | 0.00 | 0.00 | 0.00 | 0.06 | 0.00 | 0.00 | 0.01 | 0.08 | 0.01 | 0.04 | 0.03 | 0.00 | 0.02 | 0.12 |
| CNR1 | ENSG00000118432 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.37 | 0.03 | 0.07 | 0.00 | 0.00 | 0.01 | 0.04 | 0.01 | 0.06 | 0.09 | 0.03 | 0.02 | 0.03 | 0.03 | 0.06 | 0.02 | 0.08 | 0.00 | 0.02 | 0.01 | 0.02 | 0.00 | 0.03 | 0.01 | 0.06 | 0.00 | 0.11 | 0.12 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.10 | 0.16 | 0.12 | 0.02 | 0.01 | 0.02 | 0.01 | 0.15 | 0.07 | 0.04 | 0.13 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.22 | 0.00 | 0.01 | 0.00 | 0.03 | 0.06 | 0.03 | 0.02 | 0.04 |
| ALDH8A1 | ENSG00000118514 | 0.00 | 0.05 | 0.00 | 0.00 | 0.00 | 0.05 | 0.01 | 0.01 | 0.12 | 0.04 | 0.00 | 0.01 | 0.00 | 0.14 | 0.03 | 0.05 | 0.07 | 0.03 | 0.05 | 0.02 | 0.16 | 0.01 | 0.12 | 0.01 | 0.02 | 0.01 | 0.04 | 0.02 | 0.04 | 0.02 | 0.00 | 0.08 | 0.00 | 0.10 | 0.09 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.14 | 0.06 | 0.06 | 0.29 | 0.04 | 0.03 | 0.04 | 0.02 | 0.12 | 0.03 | 0.28 | 0.04 | 0.01 | 0.04 | 0.00 | 0.00 | 0.00 | 0.16 | 0.00 | 0.05 | 0.00 | 0.11 | 0.00 | 0.09 | 0.01 | 0.13 |
| CTGF | ENSG00000118523 | 0.00 | 0.05 | 0.00 | 0.00 | 0.00 | 0.05 | 0.01 | 0.02 | 0.07 | 0.05 | 0.00 | 0.01 | 0.00 | 0.13 | 0.03 | 0.04 | 0.06 | 0.03 | 0.04 | 0.02 | 0.10 | 0.02 | 0.06 | 0.04 | 0.02 | 0.01 | 0.04 | 0.03 | 0.00 | 0.02 | 0.01 | 0.09 | 0.00 | 0.10 | 0.04 | 0.04 | 0.00 | 0.01 | 0.00 | 0.00 | 0.11 | 0.04 | 0.07 | 0.28 | 0.01 | 0.02 | 0.06 | 0.02 | 0.08 | 0.03 | 0.25 | 0.05 | 0.01 | 0.04 | 0.00 | 0.00 | 0.00 | 0.15 | 0.00 | 0.05 | 0.00 | 0.10 | 0.00 | 0.09 | 0.01 | 0.12 |
| VAMP8 | ENSG00000118640 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.02 | 0.09 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.04 | 0.01 | 0.13 | 0.01 | 0.08 | 0.01 | 0.12 | 0.01 | 0.06 | 0.01 | 0.00 | 0.01 | 0.01 | 0.01 | 0.01 | 0.01 | 0.04 | 0.02 | 0.00 | 0.02 | 0.04 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.05 | 0.02 | 0.14 | 0.04 | 0.07 | 0.00 | 0.08 | 0.01 | 0.15 | 0.03 | 0.26 | 0.03 | 0.03 | 0.04 | 0.00 | 0.00 | 0.04 | 0.04 | 0.00 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 |
| GHRH | ENSG00000118702 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.01 | 0.03 | 0.07 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.02 | 0.11 | 0.01 | 0.04 | 0.01 | 0.11 | 0.01 | 0.08 | 0.00 | 0.07 | 0.00 | 0.18 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.00 | 0.04 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.10 | 0.02 | 0.11 | 0.06 | 0.05 | 0.01 | 0.07 | 0.01 | 0.18 | 0.00 | 0.07 | 0.05 | 0.00 | 0.01 | 0.00 | 0.03 | 0.01 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.04 | 0.00 |
| OLFM3 | ENSG00000118733 | 0.00 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.02 | 0.07 | 0.02 | 0.07 | 0.00 | 0.00 | 0.00 | 0.34 | 0.03 | 0.12 | 0.02 | 0.10 | 0.01 | 0.08 | 0.02 | 0.10 | 0.01 | 0.07 | 0.00 | 0.08 | 0.01 | 0.05 | 0.00 | 0.02 | 0.02 | 0.03 | 0.00 | 0.11 | 0.04 | 0.04 | 0.00 | 0.27 | 0.00 | 0.00 | 0.03 | 0.11 | 0.14 | 0.18 | 0.01 | 0.07 | 0.02 | 0.03 | 0.01 | 0.06 | 0.06 | 0.09 | 0.03 | 0.05 | 0.00 | 0.00 | 0.00 | 0.07 | 0.01 | 0.01 | 0.01 | 0.03 | 0.00 | 0.03 | 0.04 | 0.11 |
| ABCG2 | ENSG00000118777 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.03 | 0.03 | 0.12 | 0.05 | 0.00 | 0.00 | 0.02 | 0.07 | 0.02 | 0.03 | 0.06 | 0.04 | 0.04 | 0.02 | 0.04 | 0.08 | 0.03 | 0.06 | 0.01 | 0.02 | 0.00 | 0.01 | 0.00 | 0.01 | 0.03 | 0.11 | 0.00 | 0.03 | 0.04 | 0.02 | 0.02 | 0.02 | 0.00 | 0.00 | 0.04 | 0.04 | 0.04 | 0.23 | 0.01 | 0.03 | 0.02 | 0.02 | 0.07 | 0.09 | 0.05 | 0.07 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.05 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.05 |
| EEF2KMT | ENSG00000118894 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.01 | 0.15 | 0.00 | 0.00 | 0.05 | 0.02 | 0.04 | 0.03 | 0.06 | 0.08 | 0.04 | 0.03 | 0.02 | 0.07 | 0.03 | 0.06 | 0.03 | 0.03 | 0.02 | 0.02 | 0.02 | 0.02 | 0.03 | 0.03 | 0.05 | 0.05 | 0.12 | 0.02 | 0.01 | 0.01 | 0.00 | 0.00 | 0.08 | 0.02 | 0.15 | 0.15 | 0.11 | 0.01 | 0.04 | 0.02 | 0.06 | 0.12 | 0.10 | 0.06 | 0.00 | 0.00 | 0.00 | 0.00 | 0.09 | 0.00 | 0.01 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.06 | 0.01 |
| UCHL3 | ENSG00000118939 | 0.01 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.24 | 0.14 | 0.10 | 0.00 | 0.02 | 0.00 | 0.06 | 0.09 | 0.05 | 0.07 | 0.06 | 0.11 | 0.04 | 0.07 | 0.05 | 0.11 | 0.03 | 0.10 | 0.01 | 0.17 | 0.03 | 0.01 | 0.01 | 0.07 | 0.13 | 0.00 | 0.17 | 0.02 | 0.02 | 0.00 | 0.00 | 0.00 | 0.01 | 0.05 | 0.07 | 0.14 | 0.11 | 0.13 | 0.07 | 0.03 | 0.04 | 0.33 | 0.11 | 0.13 | 0.20 | 0.00 | 0.02 | 0.00 | 0.00 | 0.04 | 0.11 | 0.00 | 0.07 | 0.02 | 0.09 | 0.05 | 0.00 | 0.04 | 0.02 |
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