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 |
| TRPV3 | ENSG00000167723 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.06 | 0.04 | 0.03 | 0.00 | 0.00 | 0.01 | 0.02 | 0.01 | 0.06 | 0.02 | 0.02 | 0.01 | 0.03 | 0.04 | 0.04 | 0.02 | 0.02 | 0.01 | 0.01 | 0.00 | 0.01 | 0.00 | 0.03 | 0.01 | 0.13 | 0.02 | 0.08 | 0.02 | 0.03 | 0.00 | 0.03 | 0.00 | 0.00 | 0.03 | 0.05 | 0.13 | 0.09 | 0.01 | 0.03 | 0.04 | 0.04 | 0.06 | 0.13 | 0.15 | 0.23 | 0.00 | 0.02 | 0.00 | 0.03 | 0.00 | 0.06 | 0.00 | 0.00 | 0.00 | 0.06 | 0.00 | 0.00 | 0.03 | 0.03 |
| GPR162 | ENSG00000250510 | 0.01 | 0.00 | 0.00 | 0.01 | 0.02 | 0.00 | 0.01 | 0.07 | 0.09 | 0.02 | 0.01 | 0.00 | 0.00 | 0.08 | 0.07 | 0.07 | 0.17 | 0.01 | 0.11 | 0.01 | 0.08 | 0.02 | 0.06 | 0.05 | 0.06 | 0.02 | 0.05 | 0.04 | 0.06 | 0.07 | 0.03 | 0.04 | 0.18 | 0.05 | 0.06 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.13 | 0.04 | 0.35 | 0.07 | 0.03 | 0.02 | 0.09 | 0.02 | 0.18 | 0.03 | 0.08 | 0.11 | 0.60 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.15 | 0.01 | 0.05 | 0.01 | 0.00 | 0.01 | 0.04 | 0.04 |
| NLRP3 | ENSG00000162711 | 0.01 | 0.02 | 0.01 | 0.01 | 0.00 | 0.01 | 0.02 | 0.03 | 0.14 | 0.04 | 0.02 | 0.02 | 0.08 | 0.04 | 0.13 | 0.01 | 0.17 | 0.02 | 0.09 | 0.01 | 0.27 | 0.04 | 0.14 | 0.01 | 0.04 | 0.02 | 0.07 | 0.02 | 0.02 | 0.01 | 0.20 | 0.02 | 0.23 | 0.02 | 0.10 | 0.07 | 0.00 | 0.04 | 0.00 | 0.00 | 0.29 | 0.02 | 0.48 | 0.11 | 0.13 | 0.01 | 0.12 | 0.02 | 0.32 | 0.00 | 0.11 | 0.25 | 0.06 | 0.02 | 0.01 | 0.00 | 0.03 | 0.18 | 0.01 | 0.04 | 0.02 | 0.04 | 0.13 | 0.03 | 0.25 | 0.02 |
| PTPN12 | ENSG00000127947 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.04 | 0.02 | 0.00 | 0.00 | 0.02 | 0.01 | 0.04 | 0.02 | 0.11 | 0.03 | 0.06 | 0.02 | 0.16 | 0.03 | 0.09 | 0.02 | 0.01 | 0.01 | 0.01 | 0.00 | 0.02 | 0.01 | 0.06 | 0.01 | 0.00 | 0.01 | 0.03 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.06 | 0.02 | 0.17 | 0.09 | 0.04 | 0.01 | 0.05 | 0.02 | 0.12 | 0.07 | 0.03 | 0.07 | 0.09 | 0.00 | 0.00 | 0.00 | 0.10 | 0.00 | 0.03 | 0.01 | 0.05 | 0.01 | 0.00 | 0.00 | 0.05 | 0.02 |
| SLC1A2 | ENSG00000110436 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.05 | 0.14 | 0.03 | 0.00 | 0.00 | 0.03 | 0.04 | 0.07 | 0.02 | 0.15 | 0.02 | 0.18 | 0.00 | 0.27 | 0.04 | 0.26 | 0.00 | 0.01 | 0.01 | 0.01 | 0.00 | 0.02 | 0.01 | 0.03 | 0.00 | 0.00 | 0.02 | 0.04 | 0.01 | 0.02 | 0.05 | 0.00 | 0.00 | 0.16 | 0.01 | 0.18 | 0.07 | 0.14 | 0.01 | 0.06 | 0.02 | 0.07 | 0.02 | 0.15 | 0.09 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.03 | 0.02 | 0.00 | 0.02 | 0.05 | 0.01 |
| ACVR2A | ENSG00000121989 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.17 | 0.03 | 0.06 | 0.00 | 0.01 | 0.00 | 0.01 | 0.02 | 0.02 | 0.05 | 0.04 | 0.04 | 0.02 | 0.07 | 0.03 | 0.01 | 0.07 | 0.00 | 0.04 | 0.00 | 0.02 | 0.01 | 0.02 | 0.01 | 0.12 | 0.05 | 0.05 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.07 | 0.16 | 0.10 | 0.07 | 0.03 | 0.03 | 0.01 | 0.01 | 0.09 | 0.10 | 0.06 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.17 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 |
| KLHL35 | ENSG00000149243 | 0.00 | 0.01 | 0.00 | 0.00 | 0.10 | 0.00 | 0.04 | 0.00 | 0.15 | 0.03 | 0.00 | 0.00 | 0.08 | 0.00 | 0.13 | 0.02 | 0.15 | 0.02 | 0.23 | 0.03 | 0.49 | 0.02 | 0.13 | 0.02 | 0.02 | 0.00 | 0.02 | 0.01 | 0.01 | 0.01 | 0.05 | 0.01 | 0.02 | 0.02 | 0.03 | 0.00 | 0.02 | 0.02 | 0.00 | 0.00 | 0.43 | 0.06 | 0.55 | 0.02 | 0.10 | 0.01 | 0.11 | 0.01 | 0.26 | 0.13 | 0.18 | 0.04 | 0.02 | 0.03 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.24 | 0.00 |
| KCNAB2 | ENSG00000069424 | 0.00 | 0.06 | 0.01 | 0.10 | 0.00 | 0.00 | 0.01 | 0.05 | 0.10 | 0.09 | 0.00 | 0.02 | 0.04 | 0.31 | 0.07 | 0.06 | 0.07 | 0.11 | 0.06 | 0.09 | 0.17 | 0.09 | 0.09 | 0.09 | 0.02 | 0.15 | 0.00 | 0.20 | 0.05 | 0.06 | 0.02 | 0.32 | 0.00 | 1.09 | 0.03 | 0.23 | 0.01 | 0.11 | 0.00 | 0.00 | 0.03 | 0.19 | 0.26 | 0.36 | 0.06 | 0.10 | 0.06 | 0.12 | 0.11 | 0.27 | 0.17 | 0.25 | 0.08 | 0.12 | 0.02 | 0.01 | 0.00 | 0.18 | 0.00 | 0.07 | 0.02 | 0.29 | 0.00 | 0.05 | 0.06 | 0.16 |
| LINGO1 | ENSG00000169783 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.02 | 0.01 | 0.02 | 0.03 | 0.03 | 0.00 | 0.00 | 0.09 | 0.00 | 0.03 | 0.01 | 0.08 | 0.01 | 0.02 | 0.03 | 0.07 | 0.03 | 0.07 | 0.03 | 0.03 | 0.01 | 0.03 | 0.00 | 0.04 | 0.01 | 0.04 | 0.03 | 0.05 | 0.01 | 0.07 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.09 | 0.02 | 0.18 | 0.12 | 0.14 | 0.00 | 0.04 | 0.03 | 0.15 | 0.11 | 0.08 | 0.05 | 0.00 | 0.01 | 0.00 | 0.00 | 0.06 | 0.00 | 0.02 | 0.01 | 0.01 | 0.02 | 0.00 | 0.00 | 0.19 | 0.01 |
| PTGR2 | ENSG00000140043 | 0.00 | 0.03 | 0.00 | 0.01 | 0.00 | 0.01 | 0.01 | 0.05 | 0.04 | 0.05 | 0.00 | 0.01 | 0.00 | 0.08 | 0.03 | 0.05 | 0.05 | 0.03 | 0.04 | 0.01 | 0.05 | 0.02 | 0.01 | 0.05 | 0.00 | 0.03 | 0.01 | 0.03 | 0.01 | 0.01 | 0.02 | 0.10 | 0.00 | 0.33 | 0.03 | 0.05 | 0.01 | 0.03 | 0.00 | 0.00 | 0.01 | 0.10 | 0.08 | 0.20 | 0.05 | 0.02 | 0.03 | 0.02 | 0.17 | 0.06 | 0.08 | 0.15 | 0.03 | 0.01 | 0.00 | 0.00 | 0.04 | 0.00 | 0.00 | 0.11 | 0.02 | 0.08 | 0.03 | 0.00 | 0.00 | 0.05 |
| CACNA1G | ENSG00000006283 | 0.01 | 0.00 | 0.05 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.15 | 0.01 | 0.01 | 0.00 | 0.09 | 0.00 | 0.09 | 0.00 | 0.13 | 0.01 | 0.02 | 0.01 | 0.21 | 0.01 | 0.12 | 0.01 | 0.03 | 0.00 | 0.07 | 0.04 | 0.06 | 0.02 | 0.07 | 0.01 | 0.02 | 0.01 | 0.11 | 0.07 | 0.02 | 0.03 | 0.00 | 0.00 | 0.51 | 0.02 | 0.18 | 0.03 | 0.07 | 0.00 | 0.12 | 0.02 | 0.44 | 0.00 | 0.12 | 0.03 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.03 | 0.01 | 0.03 | 0.03 | 0.14 | 0.01 |
| SLC25A27 | ENSG00000153291 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.02 | 0.02 | 0.12 | 0.04 | 0.00 | 0.00 | 0.01 | 0.02 | 0.10 | 0.01 | 0.16 | 0.04 | 0.06 | 0.02 | 0.27 | 0.03 | 0.18 | 0.02 | 0.05 | 0.00 | 0.11 | 0.01 | 0.01 | 0.00 | 0.08 | 0.00 | 0.05 | 0.03 | 0.06 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.10 | 0.03 | 0.22 | 0.07 | 0.06 | 0.03 | 0.05 | 0.01 | 0.03 | 0.03 | 0.11 | 0.03 | 0.02 | 0.01 | 0.00 | 0.00 | 0.09 | 0.02 | 0.01 | 0.00 | 0.00 | 0.03 | 0.02 | 0.00 | 0.06 | 0.01 |
| AGPAT2 | ENSG00000169692 | 0.00 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.03 | 0.01 | 0.07 | 0.02 | 0.00 | 0.00 | 0.00 | 0.02 | 0.07 | 0.04 | 0.08 | 0.03 | 0.08 | 0.06 | 0.19 | 0.01 | 0.15 | 0.02 | 0.03 | 0.01 | 0.10 | 0.04 | 0.01 | 0.00 | 0.06 | 0.04 | 0.06 | 0.01 | 0.16 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.07 | 0.06 | 0.20 | 0.22 | 0.06 | 0.02 | 0.08 | 0.04 | 0.18 | 0.09 | 0.07 | 0.17 | 0.03 | 0.03 | 0.01 | 0.00 | 0.05 | 0.00 | 0.02 | 0.01 | 0.04 | 0.01 | 0.00 | 0.00 | 0.04 | 0.03 |
| CPA3 | ENSG00000163751 | 0.03 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.05 | 0.02 | 0.11 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 | 0.09 | 0.01 | 0.76 | 0.01 | 0.41 | 0.00 | 0.49 | 0.03 | 0.09 | 0.01 | 0.01 | 0.00 | 0.05 | 0.01 | 0.02 | 0.00 | 0.08 | 0.01 | 0.03 | 0.03 | 0.10 | 0.01 | 0.00 | 0.05 | 0.00 | 0.00 | 0.14 | 0.02 | 0.67 | 0.02 | 0.38 | 0.01 | 0.13 | 0.01 | 0.24 | 0.02 | 0.06 | 0.07 | 0.07 | 0.00 | 0.00 | 0.00 | 0.01 | 0.05 | 0.00 | 0.01 | 0.02 | 0.03 | 0.00 | 0.00 | 0.04 | 0.04 |
| GC | ENSG00000145321 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.00 | 0.17 | 0.02 | 0.00 | 0.00 | 0.00 | 0.07 | 0.09 | 0.03 | 0.21 | 0.01 | 0.08 | 0.01 | 0.12 | 0.03 | 0.07 | 0.02 | 0.01 | 0.01 | 0.03 | 0.01 | 0.00 | 0.01 | 0.02 | 0.07 | 0.00 | 0.03 | 0.06 | 0.00 | 0.02 | 0.02 | 0.00 | 0.00 | 0.11 | 0.02 | 0.32 | 0.09 | 0.04 | 0.03 | 0.04 | 0.02 | 0.12 | 0.05 | 0.07 | 0.05 | 0.11 | 0.00 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.02 | 0.00 | 0.02 | 0.00 | 0.00 | 0.02 | 0.02 |
| KCNQ3 | ENSG00000184156 | 0.02 | 0.00 | 0.02 | 0.00 | 0.09 | 0.00 | 0.07 | 0.02 | 0.22 | 0.03 | 0.02 | 0.01 | 0.10 | 0.02 | 0.32 | 0.01 | 0.36 | 0.00 | 0.29 | 0.01 | 0.52 | 0.01 | 0.22 | 0.01 | 0.17 | 0.01 | 0.21 | 0.01 | 0.16 | 0.00 | 0.37 | 0.01 | 0.25 | 0.01 | 0.08 | 0.00 | 0.01 | 0.02 | 0.00 | 0.00 | 0.47 | 0.03 | 1.65 | 0.02 | 0.20 | 0.00 | 0.18 | 0.01 | 0.44 | 0.03 | 0.17 | 0.06 | 0.03 | 0.02 | 0.02 | 0.00 | 0.17 | 0.02 | 0.19 | 0.01 | 0.04 | 0.02 | 0.50 | 0.00 | 0.21 | 0.00 |
| CDC42BPG | ENSG00000171219 | 0.01 | 0.00 | 0.00 | 0.01 | 0.07 | 0.00 | 0.03 | 0.01 | 0.11 | 0.01 | 0.00 | 0.00 | 0.08 | 0.00 | 0.07 | 0.03 | 0.07 | 0.02 | 0.19 | 0.02 | 0.15 | 0.04 | 0.04 | 0.03 | 0.01 | 0.02 | 0.04 | 0.04 | 0.00 | 0.03 | 0.02 | 0.04 | 0.00 | 0.11 | 0.07 | 0.07 | 0.01 | 0.01 | 0.00 | 0.00 | 0.09 | 0.09 | 0.19 | 0.04 | 0.11 | 0.01 | 0.09 | 0.03 | 0.22 | 0.06 | 0.09 | 0.03 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.05 | 0.06 |
| SLC7A7 | ENSG00000155465 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.12 | 0.07 | 0.01 | 0.00 | 0.00 | 0.02 | 0.16 | 0.03 | 0.13 | 0.07 | 0.07 | 0.07 | 0.09 | 0.07 | 0.07 | 0.04 | 0.03 | 0.02 | 0.01 | 0.07 | 0.01 | 0.04 | 0.08 | 0.00 | 0.00 | 0.02 | 0.27 | 0.05 | 0.00 | 0.03 | 0.00 | 0.00 | 0.12 | 0.03 | 0.29 | 0.12 | 0.08 | 0.02 | 0.06 | 0.03 | 0.08 | 0.07 | 0.16 | 0.05 | 0.02 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.03 | 0.03 | 0.02 | 0.10 | 0.00 | 0.00 | 0.03 | 0.02 |
| PRKACA | ENSG00000072062 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.02 | 0.05 | 0.00 | 0.00 | 0.06 | 0.02 | 0.00 | 0.05 | 0.12 | 0.04 | 0.07 | 0.02 | 0.12 | 0.04 | 0.05 | 0.02 | 0.01 | 0.00 | 0.01 | 0.03 | 0.01 | 0.01 | 0.07 | 0.06 | 0.00 | 0.03 | 0.18 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.09 | 0.03 | 0.85 | 0.06 | 0.09 | 0.01 | 0.20 | 0.02 | 0.21 | 0.11 | 0.25 | 0.02 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.06 | 0.01 | 0.00 | 0.02 | 0.00 | 0.02 | 0.00 | 0.02 | 0.02 |
| WNT11 | ENSG00000085741 | 0.01 | 0.01 | 0.00 | 0.00 | 0.09 | 0.00 | 0.05 | 0.00 | 0.18 | 0.03 | 0.00 | 0.00 | 0.08 | 0.00 | 0.13 | 0.01 | 0.15 | 0.02 | 0.22 | 0.04 | 0.34 | 0.02 | 0.12 | 0.01 | 0.01 | 0.00 | 0.03 | 0.02 | 0.01 | 0.01 | 0.05 | 0.01 | 0.24 | 0.02 | 0.03 | 0.00 | 0.02 | 0.02 | 0.00 | 0.00 | 0.45 | 0.05 | 0.65 | 0.02 | 0.11 | 0.01 | 0.14 | 0.01 | 0.27 | 0.10 | 0.20 | 0.04 | 0.02 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.01 | 0.02 | 0.00 | 0.00 | 0.23 | 0.00 |
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