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 |
| CCL20 | ENSG00000115009 | 0.01 | 0.07 | 0.04 | 0.04 | 0.00 | 0.05 | 0.01 | 0.02 | 0.00 | 0.33 | 0.00 | 0.03 | 0.00 | 0.10 | 0.03 | 0.04 | 0.01 | 0.19 | 0.01 | 0.18 | 0.05 | 0.14 | 0.05 | 0.04 | 0.02 | 0.02 | 0.04 | 0.02 | 0.05 | 0.02 | 0.04 | 0.05 | 0.00 | 0.04 | 0.03 | 0.03 | 0.00 | 0.01 | 0.00 | 0.01 | 0.03 | 0.08 | 0.18 | 0.19 | 0.01 | 0.36 | 0.03 | 0.05 | 0.17 | 0.06 | 0.10 | 0.27 | 0.06 | 0.03 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.05 | 0.00 | 0.00 | 0.02 | 0.05 | 0.02 | 0.07 |
| SLC35F5 | ENSG00000115084 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.06 | 0.05 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.01 | 0.11 | 0.01 | 0.08 | 0.01 | 0.20 | 0.02 | 0.07 | 0.02 | 0.00 | 0.01 | 0.00 | 0.01 | 0.01 | 0.01 | 0.02 | 0.03 | 0.00 | 0.01 | 0.05 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.03 | 0.19 | 0.10 | 0.04 | 0.01 | 0.15 | 0.01 | 0.27 | 0.00 | 0.11 | 0.01 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.08 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 |
| ZAP70 | ENSG00000115085 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 | 0.14 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.07 | 0.01 | 0.15 | 0.01 | 0.15 | 0.01 | 0.24 | 0.02 | 0.08 | 0.01 | 0.01 | 0.01 | 0.05 | 0.01 | 0.00 | 0.01 | 0.02 | 0.00 | 0.00 | 0.01 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.02 | 0.21 | 0.05 | 0.03 | 0.01 | 0.05 | 0.01 | 0.16 | 0.00 | 0.15 | 0.03 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.06 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 |
| TP53I3 | ENSG00000115129 | 0.00 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 | 0.09 | 0.01 | 0.00 | 0.00 | 0.03 | 0.08 | 0.05 | 0.01 | 0.08 | 0.02 | 0.04 | 0.02 | 0.06 | 0.05 | 0.03 | 0.03 | 0.01 | 0.00 | 0.01 | 0.02 | 0.01 | 0.04 | 0.08 | 0.01 | 0.00 | 0.05 | 0.01 | 0.04 | 0.01 | 0.00 | 0.00 | 0.00 | 0.05 | 0.04 | 0.17 | 0.12 | 0.08 | 0.00 | 0.11 | 0.02 | 0.30 | 0.03 | 0.05 | 0.10 | 0.17 | 0.01 | 0.00 | 0.00 | 0.02 | 0.03 | 0.01 | 0.01 | 0.02 | 0.03 | 0.05 | 0.00 | 0.02 | 0.04 |
| POMC | ENSG00000115138 | 0.00 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.02 | 0.02 | 0.08 | 0.01 | 0.00 | 0.00 | 0.03 | 0.08 | 0.05 | 0.01 | 0.09 | 0.01 | 0.03 | 0.01 | 0.06 | 0.04 | 0.03 | 0.03 | 0.01 | 0.00 | 0.01 | 0.02 | 0.01 | 0.04 | 0.09 | 0.01 | 0.00 | 0.05 | 0.01 | 0.04 | 0.01 | 0.00 | 0.00 | 0.00 | 0.05 | 0.04 | 0.16 | 0.12 | 0.08 | 0.00 | 0.10 | 0.02 | 0.25 | 0.03 | 0.03 | 0.10 | 0.17 | 0.01 | 0.00 | 0.01 | 0.02 | 0.06 | 0.00 | 0.01 | 0.01 | 0.03 | 0.05 | 0.00 | 0.01 | 0.04 |
| SLC30A3 | ENSG00000115194 | 0.00 | 0.00 | 0.04 | 0.01 | 0.00 | 0.00 | 0.01 | 0.01 | 0.08 | 0.01 | 0.00 | 0.00 | 0.03 | 0.07 | 0.06 | 0.01 | 0.10 | 0.01 | 0.03 | 0.01 | 0.05 | 0.05 | 0.04 | 0.03 | 0.00 | 0.00 | 0.02 | 0.02 | 0.01 | 0.04 | 0.11 | 0.00 | 0.00 | 0.05 | 0.06 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.03 | 0.22 | 0.07 | 0.08 | 0.00 | 0.12 | 0.02 | 0.25 | 0.00 | 0.04 | 0.08 | 0.17 | 0.01 | 0.00 | 0.00 | 0.02 | 0.02 | 0.00 | 0.00 | 0.01 | 0.02 | 0.05 | 0.00 | 0.03 | 0.03 |
| PCSK4 | ENSG00000115257 | 0.00 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.04 | 0.03 | 0.14 | 0.02 | 0.00 | 0.03 | 0.10 | 0.02 | 0.09 | 0.03 | 0.14 | 0.01 | 0.14 | 0.01 | 0.17 | 0.04 | 0.08 | 0.01 | 0.07 | 0.02 | 0.09 | 0.00 | 0.07 | 0.03 | 0.14 | 0.05 | 0.03 | 0.08 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.01 | 0.18 | 0.03 | 0.93 | 0.03 | 0.24 | 0.00 | 0.26 | 0.03 | 0.69 | 0.23 | 0.19 | 0.00 | 0.00 | 0.00 | 0.02 | 0.02 | 0.00 | 0.03 | 0.02 | 0.05 | 0.01 | 0.02 | 0.02 | 0.04 | 0.08 |
| GCG | ENSG00000115263 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.02 | 0.08 | 0.08 | 0.03 | 0.00 | 0.01 | 0.00 | 0.00 | 0.06 | 0.01 | 0.10 | 0.02 | 0.05 | 0.02 | 0.10 | 0.03 | 0.03 | 0.04 | 0.01 | 0.02 | 0.01 | 0.02 | 0.05 | 0.01 | 0.05 | 0.06 | 0.00 | 0.05 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.03 | 0.28 | 0.05 | 0.05 | 0.01 | 0.05 | 0.01 | 0.03 | 0.00 | 0.06 | 0.08 | 0.03 | 0.01 | 0.00 | 0.00 | 0.00 | 0.15 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.04 | 0.01 |
| HTRA2 | ENSG00000115317 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.04 | 0.11 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.03 | 0.01 | 0.13 | 0.00 | 0.05 | 0.00 | 0.07 | 0.01 | 0.03 | 0.01 | 0.01 | 0.01 | 0.01 | 0.01 | 0.00 | 0.01 | 0.01 | 0.02 | 0.00 | 0.02 | 0.03 | 0.03 | 0.00 | 0.01 | 0.00 | 0.00 | 0.06 | 0.02 | 0.16 | 0.04 | 0.03 | 0.00 | 0.05 | 0.01 | 0.10 | 0.03 | 0.06 | 0.04 | 0.04 | 0.05 | 0.00 | 0.00 | 0.04 | 0.06 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 |
| KCNJ13 | ENSG00000115474 | 0.01 | 0.08 | 0.04 | 0.04 | 0.00 | 0.05 | 0.01 | 0.05 | 0.00 | 0.35 | 0.00 | 0.03 | 0.00 | 0.07 | 0.04 | 0.04 | 0.02 | 0.20 | 0.01 | 0.18 | 0.03 | 0.17 | 0.03 | 0.08 | 0.02 | 0.04 | 0.02 | 0.02 | 0.04 | 0.03 | 0.03 | 0.06 | 0.05 | 0.01 | 0.02 | 0.07 | 0.00 | 0.01 | 0.00 | 0.01 | 0.02 | 0.10 | 0.15 | 0.22 | 0.01 | 0.39 | 0.05 | 0.06 | 0.13 | 0.06 | 0.04 | 0.35 | 0.05 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.13 | 0.00 | 0.07 | 0.01 | 0.08 | 0.01 | 0.11 |
| TXNDC9 | ENSG00000115514 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.01 | 0.14 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.06 | 0.01 | 0.13 | 0.02 | 0.08 | 0.02 | 0.19 | 0.01 | 0.05 | 0.02 | 0.01 | 0.00 | 0.04 | 0.00 | 0.00 | 0.01 | 0.01 | 0.01 | 0.00 | 0.01 | 0.03 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.02 | 0.16 | 0.06 | 0.03 | 0.02 | 0.05 | 0.01 | 0.17 | 0.00 | 0.14 | 0.04 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.06 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 |
| GNLY | ENSG00000115523 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.06 | 0.02 | 0.03 | 0.09 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.05 | 0.01 | 0.12 | 0.01 | 0.08 | 0.01 | 0.11 | 0.01 | 0.05 | 0.01 | 0.00 | 0.01 | 0.01 | 0.01 | 0.01 | 0.01 | 0.04 | 0.02 | 0.00 | 0.02 | 0.06 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.05 | 0.02 | 0.12 | 0.04 | 0.05 | 0.00 | 0.07 | 0.01 | 0.19 | 0.03 | 0.25 | 0.03 | 0.03 | 0.04 | 0.00 | 0.00 | 0.04 | 0.04 | 0.00 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 |
| PRKAG3 | ENSG00000115592 | 0.01 | 0.06 | 0.04 | 0.04 | 0.00 | 0.03 | 0.01 | 0.02 | 0.01 | 0.27 | 0.00 | 0.01 | 0.00 | 0.10 | 0.02 | 0.03 | 0.04 | 0.19 | 0.00 | 0.18 | 0.03 | 0.11 | 0.06 | 0.04 | 0.02 | 0.01 | 0.02 | 0.02 | 0.05 | 0.03 | 0.03 | 0.04 | 0.00 | 0.01 | 0.04 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.04 | 0.06 | 0.18 | 0.15 | 0.04 | 0.34 | 0.06 | 0.04 | 0.19 | 0.05 | 0.08 | 0.19 | 0.08 | 0.01 | 0.00 | 0.00 | 0.00 | 0.04 | 0.01 | 0.02 | 0.01 | 0.00 | 0.02 | 0.02 | 0.03 | 0.03 |
| WNT6 | ENSG00000115596 | 0.01 | 0.06 | 0.04 | 0.04 | 0.00 | 0.03 | 0.01 | 0.02 | 0.01 | 0.27 | 0.00 | 0.01 | 0.00 | 0.10 | 0.02 | 0.03 | 0.04 | 0.19 | 0.00 | 0.18 | 0.03 | 0.11 | 0.06 | 0.04 | 0.02 | 0.01 | 0.02 | 0.02 | 0.05 | 0.03 | 0.03 | 0.04 | 0.00 | 0.01 | 0.04 | 0.02 | 0.01 | 0.00 | 0.00 | 0.01 | 0.04 | 0.06 | 0.18 | 0.15 | 0.04 | 0.34 | 0.06 | 0.04 | 0.19 | 0.05 | 0.08 | 0.19 | 0.08 | 0.01 | 0.00 | 0.00 | 0.00 | 0.04 | 0.01 | 0.02 | 0.01 | 0.00 | 0.02 | 0.02 | 0.03 | 0.03 |
| IL1RL1 | ENSG00000115602 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.01 | 0.10 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.02 | 0.10 | 0.01 | 0.07 | 0.01 | 0.20 | 0.02 | 0.07 | 0.02 | 0.00 | 0.01 | 0.02 | 0.00 | 0.01 | 0.01 | 0.01 | 0.02 | 0.00 | 0.01 | 0.05 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.03 | 0.16 | 0.07 | 0.03 | 0.01 | 0.05 | 0.01 | 0.09 | 0.00 | 0.13 | 0.04 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 |
| SLC9A2 | ENSG00000115616 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.01 | 0.09 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.03 | 0.02 | 0.10 | 0.01 | 0.07 | 0.01 | 0.19 | 0.02 | 0.08 | 0.02 | 0.01 | 0.00 | 0.02 | 0.00 | 0.01 | 0.01 | 0.01 | 0.02 | 0.00 | 0.01 | 0.03 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.02 | 0.15 | 0.07 | 0.03 | 0.01 | 0.04 | 0.01 | 0.09 | 0.00 | 0.15 | 0.04 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.02 | 0.00 |
| ABCB6 | ENSG00000115657 | 0.01 | 0.06 | 0.04 | 0.04 | 0.00 | 0.03 | 0.01 | 0.02 | 0.01 | 0.27 | 0.00 | 0.01 | 0.00 | 0.10 | 0.03 | 0.03 | 0.04 | 0.19 | 0.00 | 0.18 | 0.03 | 0.13 | 0.06 | 0.04 | 0.02 | 0.01 | 0.02 | 0.02 | 0.05 | 0.03 | 0.03 | 0.04 | 0.00 | 0.04 | 0.03 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.04 | 0.06 | 0.18 | 0.16 | 0.03 | 0.34 | 0.05 | 0.04 | 0.08 | 0.05 | 0.09 | 0.19 | 0.08 | 0.01 | 0.00 | 0.00 | 0.00 | 0.04 | 0.00 | 0.02 | 0.00 | 0.00 | 0.02 | 0.02 | 0.02 | 0.04 |
| STK16 | ENSG00000115661 | 0.01 | 0.07 | 0.04 | 0.04 | 0.00 | 0.03 | 0.01 | 0.02 | 0.01 | 0.27 | 0.00 | 0.01 | 0.00 | 0.10 | 0.03 | 0.03 | 0.04 | 0.19 | 0.00 | 0.18 | 0.03 | 0.13 | 0.05 | 0.04 | 0.02 | 0.01 | 0.02 | 0.02 | 0.05 | 0.03 | 0.03 | 0.04 | 0.00 | 0.04 | 0.03 | 0.03 | 0.01 | 0.00 | 0.00 | 0.01 | 0.04 | 0.06 | 0.18 | 0.16 | 0.03 | 0.34 | 0.05 | 0.04 | 0.08 | 0.05 | 0.09 | 0.19 | 0.08 | 0.01 | 0.00 | 0.00 | 0.00 | 0.04 | 0.00 | 0.02 | 0.00 | 0.00 | 0.02 | 0.02 | 0.02 | 0.04 |
| SLC5A7 | ENSG00000115665 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.02 | 0.06 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.01 | 0.10 | 0.01 | 0.07 | 0.01 | 0.16 | 0.01 | 0.06 | 0.02 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.02 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.02 | 0.10 | 0.09 | 0.04 | 0.02 | 0.04 | 0.01 | 0.06 | 0.00 | 0.13 | 0.03 | 0.02 | 0.01 | 0.00 | 0.00 | 0.04 | 0.05 | 0.00 | 0.00 | 0.02 | 0.02 | 0.00 | 0.00 | 0.03 | 0.00 |
| PROC | ENSG00000115718 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.15 | 0.05 | 0.04 | 0.00 | 0.01 | 0.00 | 0.00 | 0.03 | 0.01 | 0.08 | 0.02 | 0.06 | 0.01 | 0.09 | 0.06 | 0.03 | 0.04 | 0.00 | 0.01 | 0.01 | 0.01 | 0.01 | 0.01 | 0.02 | 0.04 | 0.00 | 0.01 | 0.07 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.05 | 0.11 | 0.18 | 0.03 | 0.00 | 0.02 | 0.01 | 0.07 | 0.00 | 0.15 | 0.03 | 0.03 | 0.01 | 0.00 | 0.00 | 0.00 | 0.12 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 |
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