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 |
| TPTE2 | ENSG00000132958 | 0.00 | 0.02 | 0.01 | 0.01 | 0.00 | 0.00 | 0.05 | 0.03 | 0.11 | 0.08 | 0.00 | 0.00 | 0.02 | 0.17 | 0.02 | 0.15 | 0.06 | 0.14 | 0.03 | 0.17 | 0.07 | 0.13 | 0.11 | 0.07 | 0.16 | 0.01 | 0.27 | 0.02 | 0.02 | 0.01 | 0.05 | 0.11 | 0.00 | 0.15 | 0.00 | 0.07 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.08 | 0.08 | 0.22 | 0.03 | 0.17 | 0.02 | 0.07 | 0.30 | 0.10 | 0.19 | 0.18 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.06 | 0.01 | 0.07 | 0.02 | 0.07 | 0.00 | 0.00 | 0.06 | 0.05 |
| IMPG1 | ENSG00000112706 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.18 | 0.02 | 0.08 | 0.00 | 0.00 | 0.01 | 0.05 | 0.04 | 0.04 | 0.08 | 0.03 | 0.03 | 0.03 | 0.06 | 0.06 | 0.05 | 0.06 | 0.00 | 0.02 | 0.02 | 0.02 | 0.01 | 0.02 | 0.02 | 0.04 | 0.00 | 0.22 | 0.06 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.08 | 0.15 | 0.10 | 0.01 | 0.01 | 0.04 | 0.01 | 0.13 | 0.08 | 0.04 | 0.15 | 0.03 | 0.00 | 0.00 | 0.00 | 0.01 | 0.17 | 0.00 | 0.01 | 0.00 | 0.05 | 0.06 | 0.06 | 0.03 | 0.04 |
| IL1RAPL1 | ENSG00000169306 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.03 | 0.02 | 0.07 | 0.03 | 0.00 | 0.00 | 0.00 | 0.02 | 0.02 | 0.05 | 0.07 | 0.08 | 0.02 | 0.13 | 0.11 | 0.10 | 0.05 | 0.03 | 0.01 | 0.02 | 0.06 | 0.01 | 0.00 | 0.01 | 0.00 | 0.02 | 0.00 | 0.01 | 0.04 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.04 | 0.02 | 0.09 | 0.19 | 0.04 | 0.05 | 0.03 | 0.03 | 0.09 | 0.16 | 0.24 | 0.06 | 0.05 | 0.02 | 0.00 | 0.00 | 0.09 | 0.00 | 0.01 | 0.02 | 0.05 | 0.02 | 0.00 | 0.00 | 0.03 | 0.01 |
| OR13A1 | ENSG00000256574 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.04 | 0.09 | 0.04 | 0.07 | 0.00 | 0.01 | 0.04 | 0.05 | 0.02 | 0.09 | 0.02 | 0.04 | 0.03 | 0.10 | 0.06 | 0.04 | 0.02 | 0.00 | 0.02 | 0.00 | 0.01 | 0.00 | 0.01 | 0.02 | 0.01 | 0.15 | 0.01 | 0.07 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.07 | 0.04 | 0.08 | 0.11 | 0.01 | 0.02 | 0.02 | 0.03 | 0.05 | 0.03 | 0.06 | 0.10 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.02 | 0.01 | 0.02 | 0.01 | 0.00 | 0.00 | 0.01 | 0.03 |
| CYP3A43 | ENSG00000021461 | 0.01 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.04 | 0.02 | 0.08 | 0.01 | 0.00 | 0.00 | 0.03 | 0.03 | 0.12 | 0.02 | 0.24 | 0.01 | 0.24 | 0.00 | 0.52 | 0.02 | 0.33 | 0.01 | 0.02 | 0.01 | 0.02 | 0.00 | 0.11 | 0.01 | 0.10 | 0.01 | 0.11 | 0.01 | 0.10 | 0.03 | 0.01 | 0.02 | 0.00 | 0.00 | 0.07 | 0.03 | 0.21 | 0.05 | 0.07 | 0.01 | 0.07 | 0.02 | 0.15 | 0.03 | 0.07 | 0.04 | 0.09 | 0.01 | 0.00 | 0.00 | 0.13 | 0.00 | 0.06 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.04 | 0.03 |
| TGM7 | ENSG00000159495 | 0.00 | 0.01 | 0.00 | 0.02 | 0.14 | 0.00 | 0.01 | 0.06 | 0.02 | 0.06 | 0.00 | 0.00 | 0.02 | 0.33 | 0.00 | 0.09 | 0.01 | 0.08 | 0.02 | 0.04 | 0.04 | 0.05 | 0.02 | 0.07 | 0.01 | 0.08 | 0.00 | 0.06 | 0.00 | 0.04 | 0.00 | 0.02 | 0.00 | 0.07 | 0.02 | 0.09 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.10 | 0.05 | 0.34 | 0.01 | 0.09 | 0.02 | 0.08 | 0.13 | 0.30 | 0.06 | 0.07 | 0.01 | 0.03 | 0.00 | 0.00 | 0.02 | 0.15 | 0.00 | 0.02 | 0.01 | 0.11 | 0.00 | 0.00 | 0.01 | 0.17 |
| P2RX3 | ENSG00000109991 | 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 | 0.05 | 0.03 | 0.09 | 0.02 | 0.12 | 0.01 | 0.14 | 0.04 | 0.00 | 0.04 | 0.01 | 0.01 | 0.01 | 0.03 | 0.00 | 0.02 | 0.03 | 0.02 | 0.00 | 0.12 | 0.04 | 0.00 | 0.02 | 0.03 | 0.00 | 0.00 | 0.11 | 0.06 | 0.12 | 0.05 | 0.07 | 0.02 | 0.05 | 0.02 | 0.31 | 0.11 | 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 | 0.05 | 0.02 |
| CYP2C19 | ENSG00000165841 | 0.00 | 0.02 | 0.00 | 0.01 | 0.00 | 0.05 | 0.01 | 0.11 | 0.02 | 0.10 | 0.00 | 0.02 | 0.00 | 0.16 | 0.01 | 0.03 | 0.03 | 0.07 | 0.00 | 0.06 | 0.02 | 0.08 | 0.01 | 0.10 | 0.00 | 0.10 | 0.00 | 0.06 | 0.01 | 0.03 | 0.01 | 0.07 | 0.16 | 0.07 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.01 | 0.02 | 0.08 | 0.08 | 0.30 | 0.00 | 0.06 | 0.02 | 0.10 | 0.03 | 0.09 | 0.03 | 0.06 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.07 | 0.01 | 0.03 | 0.00 | 0.05 | 0.00 | 0.00 | 0.01 | 0.04 |
| BRS3 | ENSG00000102239 | 0.02 | 0.01 | 0.01 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.07 | 0.03 | 0.05 | 0.00 | 0.06 | 0.01 | 0.13 | 0.02 | 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 | 0.29 | 0.05 | 0.12 | 0.00 | 0.03 | 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 | 0.01 | 0.01 | 0.00 | 0.00 | 0.04 | 0.01 |
| AQP2 | ENSG00000167580 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.06 | 0.03 | 0.00 | 0.00 | 0.00 | 0.04 | 0.06 | 0.02 | 0.03 | 0.02 | 0.01 | 0.03 | 0.06 | 0.03 | 0.05 | 0.04 | 0.02 | 0.00 | 0.02 | 0.01 | 0.01 | 0.05 | 0.01 | 0.01 | 0.00 | 0.01 | 0.19 | 0.00 | 0.01 | 0.02 | 0.00 | 0.00 | 0.03 | 0.06 | 0.09 | 0.06 | 0.03 | 0.01 | 0.05 | 0.01 | 0.33 | 0.06 | 0.05 | 0.09 | 0.02 | 0.00 | 0.00 | 0.01 | 0.10 | 0.03 | 0.00 | 0.04 | 0.02 | 0.05 | 0.00 | 0.00 | 0.06 | 0.05 |
| WFDC8 | ENSG00000158901 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.01 | 0.16 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.05 | 0.07 | 0.01 | 0.01 | 0.01 | 0.06 | 0.00 | 0.17 | 0.00 | 0.18 | 0.00 | 0.12 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.00 | 0.01 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.14 | 0.02 | 0.21 | 0.05 | 0.02 | 0.04 | 0.10 | 0.01 | 0.29 | 0.00 | 0.11 | 0.03 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.05 | 0.01 |
| EYS | ENSG00000188107 | 0.00 | 0.01 | 0.02 | 0.01 | 0.00 | 0.00 | 0.01 | 0.10 | 0.13 | 0.06 | 0.00 | 0.00 | 0.02 | 0.05 | 0.09 | 0.06 | 0.27 | 0.04 | 0.13 | 0.03 | 0.20 | 0.05 | 0.13 | 0.05 | 0.04 | 0.02 | 0.07 | 0.00 | 0.03 | 0.03 | 0.16 | 0.03 | 0.07 | 0.24 | 0.05 | 0.02 | 0.00 | 0.04 | 0.00 | 0.00 | 0.11 | 0.06 | 0.18 | 0.10 | 0.09 | 0.02 | 0.04 | 0.01 | 0.16 | 0.05 | 0.12 | 0.09 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.04 | 0.01 | 0.02 | 0.02 | 0.03 | 0.05 | 0.03 | 0.16 | 0.03 |
| CHRM2 | ENSG00000181072 | 0.01 | 0.01 | 0.07 | 0.00 | 0.04 | 0.00 | 0.02 | 0.02 | 0.03 | 0.04 | 0.00 | 0.01 | 0.04 | 0.09 | 0.07 | 0.02 | 0.07 | 0.07 | 0.02 | 0.13 | 0.04 | 0.18 | 0.02 | 0.07 | 0.03 | 0.01 | 0.07 | 0.02 | 0.01 | 0.05 | 0.05 | 0.04 | 0.00 | 0.02 | 0.03 | 0.06 | 0.00 | 0.05 | 0.00 | 0.00 | 0.07 | 0.04 | 0.46 | 0.05 | 0.03 | 0.08 | 0.04 | 0.05 | 0.13 | 0.16 | 0.17 | 0.06 | 0.02 | 0.04 | 0.00 | 0.05 | 0.02 | 0.09 | 0.11 | 0.00 | 0.05 | 0.01 | 0.00 | 0.00 | 0.22 | 0.02 |
| KLHL1 | ENSG00000150361 | 0.01 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.27 | 0.13 | 0.13 | 0.00 | 0.02 | 0.00 | 0.08 | 0.06 | 0.05 | 0.05 | 0.09 | 0.07 | 0.08 | 0.05 | 0.06 | 0.13 | 0.04 | 0.11 | 0.01 | 0.13 | 0.01 | 0.00 | 0.01 | 0.07 | 0.15 | 0.00 | 0.17 | 0.01 | 0.01 | 0.00 | 0.01 | 0.00 | 0.01 | 0.04 | 0.08 | 0.12 | 0.13 | 0.11 | 0.08 | 0.03 | 0.03 | 0.11 | 0.13 | 0.16 | 0.22 | 0.00 | 0.02 | 0.00 | 0.00 | 0.04 | 0.10 | 0.00 | 0.07 | 0.01 | 0.12 | 0.05 | 0.00 | 0.04 | 0.03 |
| MORC1 | ENSG00000114487 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.04 | 0.03 | 0.02 | 0.00 | 0.01 | 0.00 | 0.02 | 0.05 | 0.01 | 0.18 | 0.03 | 0.05 | 0.01 | 0.07 | 0.03 | 0.06 | 0.02 | 0.00 | 0.01 | 0.01 | 0.02 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.01 | 0.10 | 0.02 | 0.00 | 0.06 | 0.00 | 0.00 | 0.05 | 0.02 | 0.31 | 0.03 | 0.04 | 0.01 | 0.03 | 0.01 | 0.14 | 0.08 | 0.12 | 0.06 | 0.03 | 0.01 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.03 | 0.01 | 0.04 | 0.00 | 0.00 | 0.02 | 0.04 |
| CEACAM16 | ENSG00000213892 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.02 | 0.00 | 0.03 | 0.14 | 0.02 | 0.00 | 0.00 | 0.05 | 0.05 | 0.14 | 0.04 | 0.14 | 0.08 | 0.07 | 0.02 | 0.15 | 0.07 | 0.18 | 0.01 | 0.01 | 0.02 | 0.01 | 0.02 | 0.08 | 0.02 | 0.08 | 0.03 | 0.12 | 0.03 | 0.24 | 0.03 | 0.00 | 0.02 | 0.00 | 0.00 | 0.09 | 0.05 | 0.21 | 0.29 | 0.21 | 0.03 | 0.12 | 0.04 | 0.22 | 0.17 | 0.07 | 0.15 | 0.00 | 0.04 | 0.01 | 0.00 | 0.07 | 0.06 | 0.03 | 0.12 | 0.02 | 0.09 | 0.00 | 0.00 | 0.02 | 0.02 |
| ART1 | ENSG00000129744 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.02 | 0.01 | 0.10 | 0.00 | 0.00 | 0.02 | 0.05 | 0.02 | 0.06 | 0.02 | 0.15 | 0.02 | 0.07 | 0.05 | 0.11 | 0.03 | 0.06 | 0.01 | 0.01 | 0.01 | 0.03 | 0.00 | 0.06 | 0.05 | 0.03 | 0.03 | 0.01 | 0.01 | 0.05 | 0.02 | 0.07 | 0.00 | 0.00 | 0.03 | 0.11 | 0.02 | 0.45 | 0.01 | 0.05 | 0.03 | 0.07 | 0.03 | 0.09 | 0.04 | 0.16 | 0.02 | 0.01 | 0.00 | 0.01 | 0.05 | 0.00 | 0.01 | 0.10 | 0.01 | 0.06 | 0.00 | 0.00 | 0.01 | 0.03 |
| ATP4B | ENSG00000186009 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.03 | 0.21 | 0.02 | 0.00 | 0.01 | 0.01 | 0.02 | 0.10 | 0.09 | 0.22 | 0.05 | 0.15 | 0.01 | 0.21 | 0.04 | 0.15 | 0.03 | 0.10 | 0.01 | 0.17 | 0.02 | 0.02 | 0.02 | 0.29 | 0.00 | 0.06 | 0.04 | 0.13 | 0.03 | 0.01 | 0.00 | 0.00 | 0.00 | 0.16 | 0.05 | 0.27 | 0.15 | 0.23 | 0.01 | 0.09 | 0.03 | 0.33 | 0.12 | 0.45 | 0.10 | 0.01 | 0.02 | 0.00 | 0.01 | 0.02 | 0.12 | 0.04 | 0.03 | 0.06 | 0.02 | 0.08 | 0.00 | 0.05 | 0.09 |
| NPY5R | ENSG00000164129 | 0.00 | 0.02 | 0.00 | 0.02 | 0.06 | 0.02 | 0.04 | 0.02 | 0.04 | 0.13 | 0.00 | 0.01 | 0.00 | 0.02 | 0.01 | 0.08 | 0.01 | 0.13 | 0.01 | 0.10 | 0.09 | 0.08 | 0.05 | 0.10 | 0.02 | 0.06 | 0.02 | 0.04 | 0.00 | 0.03 | 0.05 | 0.09 | 0.00 | 0.15 | 0.10 | 0.07 | 0.00 | 0.03 | 0.00 | 0.00 | 0.05 | 0.07 | 0.08 | 0.28 | 0.04 | 0.08 | 0.00 | 0.05 | 0.14 | 0.05 | 0.07 | 0.17 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.03 | 0.00 | 0.11 | 0.00 | 0.04 | 0.00 | 0.00 | 0.05 | 0.05 |
| CRHR2 | ENSG00000106113 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.05 | 0.00 | 0.11 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.06 | 0.00 | 0.07 | 0.02 | 0.04 | 0.02 | 0.13 | 0.03 | 0.04 | 0.00 | 0.04 | 0.00 | 0.02 | 0.00 | 0.02 | 0.00 | 0.05 | 0.00 | 0.00 | 0.02 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.09 | 0.02 | 0.16 | 0.11 | 0.02 | 0.00 | 0.06 | 0.02 | 0.04 | 0.01 | 0.17 | 0.03 | 0.05 | 0.00 | 0.00 | 0.01 | 0.00 | 0.02 | 0.02 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.06 | 0.02 |
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