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 |
| KLHL6 | ENSG00000172578 | 0.05 | 0.00 | 0.04 | 0.01 | 0.00 | 0.01 | 0.04 | 0.03 | 0.19 | 0.01 | 0.00 | 0.00 | 0.00 | 0.10 | 0.16 | 0.05 | 2.02 | 0.00 | 0.68 | 0.00 | 0.76 | 0.02 | 0.26 | 0.01 | 0.04 | 0.00 | 0.06 | 0.03 | 0.03 | 0.01 | 0.13 | 0.02 | 0.12 | 0.01 | 0.12 | 0.00 | 0.00 | 0.10 | 0.00 | 0.00 | 0.21 | 0.02 | 1.11 | 0.02 | 0.65 | 0.00 | 0.35 | 0.01 | 0.86 | 0.09 | 0.10 | 0.10 | 0.20 | 0.00 | 0.00 | 0.01 | 0.06 | 0.00 | 0.07 | 0.00 | 0.22 | 0.02 | 0.00 | 0.00 | 0.02 | 0.05 |
| SMPDL3A | ENSG00000172594 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.15 | 0.04 | 0.06 | 0.00 | 0.01 | 0.02 | 0.14 | 0.02 | 0.05 | 0.04 | 0.04 | 0.03 | 0.02 | 0.13 | 0.01 | 0.04 | 0.04 | 0.02 | 0.02 | 0.01 | 0.03 | 0.00 | 0.03 | 0.01 | 0.07 | 0.06 | 0.14 | 0.07 | 0.04 | 0.00 | 0.01 | 0.00 | 0.00 | 0.09 | 0.06 | 0.10 | 0.24 | 0.01 | 0.02 | 0.04 | 0.02 | 0.09 | 0.03 | 0.18 | 0.07 | 0.01 | 0.03 | 0.00 | 0.00 | 0.01 | 0.19 | 0.00 | 0.04 | 0.00 | 0.08 | 0.04 | 0.03 | 0.02 | 0.12 |
| OR10AD1 | ENSG00000172640 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.07 | 0.03 | 0.00 | 0.00 | 0.00 | 0.04 | 0.07 | 0.02 | 0.06 | 0.02 | 0.01 | 0.04 | 0.05 | 0.04 | 0.06 | 0.04 | 0.02 | 0.00 | 0.02 | 0.02 | 0.00 | 0.04 | 0.01 | 0.01 | 0.09 | 0.01 | 0.23 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.04 | 0.05 | 0.11 | 0.06 | 0.02 | 0.00 | 0.06 | 0.01 | 0.21 | 0.15 | 0.12 | 0.08 | 0.02 | 0.00 | 0.00 | 0.01 | 0.13 | 0.03 | 0.01 | 0.04 | 0.01 | 0.05 | 0.00 | 0.00 | 0.06 | 0.04 |
| MOS | ENSG00000172680 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.00 | 0.05 | 0.01 | 0.10 | 0.03 | 0.00 | 0.00 | 0.00 | 0.07 | 0.13 | 0.02 | 0.12 | 0.03 | 0.04 | 0.01 | 0.07 | 0.03 | 0.07 | 0.02 | 0.07 | 0.01 | 0.10 | 0.01 | 0.01 | 0.01 | 0.03 | 0.02 | 0.00 | 0.02 | 0.02 | 0.00 | 0.01 | 0.02 | 0.00 | 0.00 | 0.16 | 0.02 | 0.45 | 0.03 | 0.03 | 0.01 | 0.11 | 0.00 | 0.83 | 0.09 | 0.14 | 0.05 | 0.21 | 0.00 | 0.01 | 0.00 | 0.04 | 0.09 | 0.00 | 0.00 | 0.00 | 0.01 | 0.20 | 0.00 | 0.06 | 0.01 |
| CCL19 | ENSG00000172724 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.10 | 0.03 | 0.00 | 0.00 | 0.02 | 0.10 | 0.05 | 0.02 | 0.36 | 0.04 | 0.22 | 0.02 | 0.25 | 0.01 | 0.16 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.10 | 0.00 | 0.03 | 0.01 | 0.24 | 0.01 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.08 | 0.02 | 0.11 | 0.06 | 0.01 | 0.01 | 0.03 | 0.02 | 0.00 | 0.05 | 0.11 | 0.05 | 0.03 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.06 | 0.06 | 0.00 | 0.00 | 0.06 | 0.05 |
| OR4D9 | ENSG00000172742 | 0.01 | 0.00 | 0.00 | 0.01 | 0.09 | 0.00 | 0.02 | 0.01 | 0.10 | 0.02 | 0.00 | 0.00 | 0.07 | 0.04 | 0.04 | 0.03 | 0.07 | 0.02 | 0.10 | 0.03 | 0.07 | 0.04 | 0.02 | 0.04 | 0.01 | 0.01 | 0.03 | 0.02 | 0.00 | 0.02 | 0.01 | 0.02 | 0.04 | 0.07 | 0.06 | 0.00 | 0.02 | 0.02 | 0.00 | 0.00 | 0.10 | 0.07 | 0.12 | 0.05 | 0.05 | 0.02 | 0.05 | 0.01 | 0.13 | 0.17 | 0.05 | 0.06 | 0.00 | 0.07 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.02 | 0.01 | 0.03 | 0.00 | 0.00 | 0.06 | 0.04 |
| COL6A5 | ENSG00000172752 | 0.02 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.04 | 0.02 | 0.04 | 0.02 | 0.00 | 0.01 | 0.00 | 0.01 | 0.04 | 0.02 | 0.15 | 0.01 | 0.08 | 0.00 | 0.16 | 0.02 | 0.06 | 0.02 | 0.01 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.03 | 0.02 | 0.00 | 0.05 | 0.06 | 0.02 | 0.00 | 0.06 | 0.00 | 0.00 | 0.05 | 0.03 | 0.28 | 0.04 | 0.09 | 0.01 | 0.07 | 0.01 | 0.15 | 0.03 | 0.04 | 0.06 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.02 | 0.00 | 0.02 | 0.01 | 0.05 | 0.00 | 0.00 | 0.02 | 0.05 |
| OR5B3 | ENSG00000172769 | 0.01 | 0.00 | 0.00 | 0.01 | 0.09 | 0.00 | 0.01 | 0.02 | 0.14 | 0.02 | 0.00 | 0.00 | 0.06 | 0.03 | 0.04 | 0.04 | 0.07 | 0.02 | 0.11 | 0.02 | 0.14 | 0.05 | 0.00 | 0.04 | 0.01 | 0.00 | 0.01 | 0.03 | 0.00 | 0.02 | 0.00 | 0.03 | 0.04 | 0.07 | 0.06 | 0.00 | 0.02 | 0.03 | 0.00 | 0.00 | 0.10 | 0.07 | 0.13 | 0.05 | 0.05 | 0.02 | 0.06 | 0.01 | 0.16 | 0.13 | 0.06 | 0.04 | 0.01 | 0.05 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.01 | 0.01 | 0.03 | 0.00 | 0.00 | 0.09 | 0.02 |
| OR10W1 | ENSG00000172772 | 0.00 | 0.00 | 0.00 | 0.01 | 0.09 | 0.00 | 0.00 | 0.02 | 0.14 | 0.02 | 0.00 | 0.00 | 0.06 | 0.03 | 0.04 | 0.04 | 0.07 | 0.02 | 0.11 | 0.02 | 0.12 | 0.05 | 0.01 | 0.04 | 0.01 | 0.00 | 0.01 | 0.04 | 0.00 | 0.02 | 0.00 | 0.03 | 0.00 | 0.12 | 0.04 | 0.00 | 0.02 | 0.03 | 0.00 | 0.00 | 0.10 | 0.07 | 0.12 | 0.05 | 0.05 | 0.02 | 0.06 | 0.02 | 0.24 | 0.13 | 0.06 | 0.03 | 0.01 | 0.05 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.01 | 0.01 | 0.03 | 0.00 | 0.00 | 0.09 | 0.03 |
| CYP7B1 | ENSG00000172817 | 0.00 | 0.01 | 0.00 | 0.01 | 0.06 | 0.00 | 0.04 | 0.01 | 0.10 | 0.01 | 0.00 | 0.00 | 0.00 | 0.05 | 0.13 | 0.02 | 0.12 | 0.03 | 0.06 | 0.01 | 0.09 | 0.01 | 0.08 | 0.02 | 0.06 | 0.00 | 0.14 | 0.03 | 0.01 | 0.02 | 0.05 | 0.01 | 0.06 | 0.02 | 0.02 | 0.00 | 0.01 | 0.02 | 0.00 | 0.00 | 0.20 | 0.02 | 0.28 | 0.07 | 0.03 | 0.01 | 0.06 | 0.01 | 0.30 | 0.06 | 0.16 | 0.03 | 0.18 | 0.00 | 0.01 | 0.00 | 0.00 | 0.07 | 0.00 | 0.01 | 0.00 | 0.01 | 0.22 | 0.00 | 0.05 | 0.01 |
| RARG | ENSG00000172819 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.02 | 0.00 | 0.05 | 0.04 | 0.00 | 0.00 | 0.00 | 0.04 | 0.06 | 0.01 | 0.04 | 0.02 | 0.02 | 0.03 | 0.04 | 0.05 | 0.05 | 0.04 | 0.02 | 0.00 | 0.03 | 0.01 | 0.01 | 0.03 | 0.01 | 0.01 | 0.09 | 0.01 | 0.21 | 0.01 | 0.03 | 0.01 | 0.00 | 0.00 | 0.03 | 0.06 | 0.12 | 0.05 | 0.03 | 0.00 | 0.10 | 0.01 | 0.38 | 0.05 | 0.02 | 0.10 | 0.01 | 0.00 | 0.00 | 0.00 | 0.12 | 0.00 | 0.00 | 0.03 | 0.02 | 0.04 | 0.00 | 0.00 | 0.02 | 0.06 |
| CES3 | ENSG00000172828 | 0.01 | 0.01 | 0.02 | 0.00 | 0.00 | 0.06 | 0.00 | 0.06 | 0.10 | 0.03 | 0.00 | 0.00 | 0.03 | 0.06 | 0.04 | 0.02 | 0.05 | 0.01 | 0.03 | 0.01 | 0.12 | 0.00 | 0.04 | 0.02 | 0.00 | 0.00 | 0.02 | 0.01 | 0.01 | 0.00 | 0.03 | 0.04 | 0.05 | 0.01 | 0.23 | 0.03 | 0.01 | 0.02 | 0.00 | 0.01 | 0.02 | 0.05 | 0.05 | 0.30 | 0.03 | 0.04 | 0.05 | 0.08 | 0.05 | 0.14 | 0.03 | 0.04 | 0.15 | 0.01 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.00 | 0.03 | 0.04 | 0.01 |
| EGFL7 | ENSG00000172889 | 0.00 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.03 | 0.01 | 0.08 | 0.02 | 0.00 | 0.00 | 0.00 | 0.02 | 0.08 | 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 | 0.07 | 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 | 0.07 | 0.02 | 0.09 | 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 |
| LVRN | ENSG00000172901 | 0.22 | 0.01 | 0.03 | 0.01 | 0.00 | 0.00 | 0.01 | 0.13 | 0.05 | 0.08 | 0.00 | 0.01 | 0.00 | 0.09 | 0.01 | 0.07 | 0.00 | 0.08 | 0.01 | 0.05 | 0.02 | 0.07 | 0.02 | 0.12 | 0.01 | 0.11 | 0.01 | 0.08 | 0.00 | 0.03 | 0.06 | 0.04 | 0.05 | 0.02 | 0.16 | 0.04 | 0.00 | 0.05 | 0.00 | 0.00 | 0.02 | 0.06 | 0.11 | 0.35 | 0.00 | 0.05 | 0.01 | 0.03 | 0.01 | 0.19 | 0.09 | 0.04 | 0.01 | 0.03 | 0.00 | 0.09 | 0.04 | 0.02 | 0.00 | 0.03 | 0.00 | 0.02 | 0.00 | 0.04 | 0.05 | 0.07 |
| MRGPRD | ENSG00000172938 | 0.01 | 0.00 | 0.03 | 0.01 | 0.08 | 0.02 | 0.09 | 0.00 | 0.43 | 0.02 | 0.00 | 0.00 | 0.08 | 0.00 | 0.21 | 0.01 | 0.68 | 0.01 | 1.15 | 0.01 | 1.70 | 0.02 | 0.25 | 0.03 | 0.02 | 0.02 | 0.07 | 0.02 | 0.04 | 0.01 | 0.36 | 0.01 | 0.69 | 0.05 | 0.00 | 0.01 | 0.03 | 0.00 | 0.00 | 0.00 | 0.80 | 0.02 | 0.37 | 0.04 | 0.23 | 0.01 | 0.11 | 0.02 | 0.33 | 0.06 | 0.12 | 0.05 | 0.00 | 0.05 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.01 | 0.01 | 0.04 | 0.00 | 0.00 | 0.35 | 0.02 |
| SLC22A13 | ENSG00000172940 | 0.00 | 0.18 | 0.00 | 0.01 | 0.08 | 0.00 | 0.00 | 0.01 | 0.13 | 0.04 | 0.00 | 0.03 | 0.02 | 0.28 | 0.01 | 0.04 | 0.02 | 0.05 | 0.00 | 0.04 | 0.03 | 0.04 | 0.07 | 0.07 | 0.00 | 0.02 | 0.03 | 0.02 | 0.01 | 0.02 | 0.05 | 0.02 | 0.00 | 0.20 | 0.05 | 0.02 | 0.00 | 0.03 | 0.00 | 0.00 | 0.04 | 0.08 | 0.11 | 0.16 | 0.02 | 0.04 | 0.03 | 0.04 | 0.12 | 0.15 | 0.09 | 0.06 | 0.03 | 0.04 | 0.00 | 0.01 | 0.06 | 0.09 | 0.01 | 0.03 | 0.01 | 0.03 | 0.00 | 0.03 | 0.04 | 0.05 |
| KAT5 | ENSG00000172977 | 0.01 | 0.00 | 0.00 | 0.01 | 0.07 | 0.00 | 0.08 | 0.01 | 0.20 | 0.01 | 0.00 | 0.00 | 0.08 | 0.00 | 0.09 | 0.03 | 0.09 | 0.02 | 0.30 | 0.02 | 0.18 | 0.04 | 0.07 | 0.03 | 0.01 | 0.02 | 0.02 | 0.04 | 0.00 | 0.03 | 0.02 | 0.04 | 0.00 | 0.11 | 0.07 | 0.07 | 0.03 | 0.01 | 0.00 | 0.00 | 0.14 | 0.09 | 0.23 | 0.04 | 0.13 | 0.01 | 0.07 | 0.03 | 0.20 | 0.06 | 0.13 | 0.03 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.01 | 0.01 | 0.03 | 0.00 | 0.00 | 0.08 | 0.06 |
| RELA | ENSG00000173039 | 0.01 | 0.00 | 0.00 | 0.01 | 0.07 | 0.00 | 0.08 | 0.01 | 0.20 | 0.01 | 0.00 | 0.00 | 0.08 | 0.00 | 0.09 | 0.03 | 0.09 | 0.02 | 0.30 | 0.02 | 0.18 | 0.04 | 0.07 | 0.03 | 0.01 | 0.02 | 0.02 | 0.04 | 0.00 | 0.03 | 0.02 | 0.04 | 0.00 | 0.11 | 0.07 | 0.07 | 0.03 | 0.01 | 0.00 | 0.00 | 0.14 | 0.09 | 0.23 | 0.04 | 0.13 | 0.01 | 0.07 | 0.03 | 0.20 | 0.06 | 0.13 | 0.03 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.01 | 0.01 | 0.03 | 0.00 | 0.00 | 0.08 | 0.06 |
| RXFP4 | ENSG00000173080 | 0.03 | 0.00 | 0.01 | 0.00 | 0.00 | 0.03 | 0.03 | 0.03 | 0.36 | 0.01 | 0.02 | 0.00 | 0.11 | 0.00 | 0.34 | 0.00 | 0.25 | 0.01 | 0.05 | 0.01 | 0.22 | 0.00 | 0.16 | 0.00 | 0.03 | 0.00 | 0.11 | 0.00 | 0.07 | 0.00 | 0.35 | 0.00 | 0.48 | 0.01 | 0.09 | 0.02 | 0.07 | 0.00 | 0.00 | 0.00 | 0.30 | 0.01 | 0.59 | 0.02 | 0.17 | 0.00 | 0.34 | 0.00 | 1.11 | 0.00 | 0.35 | 0.01 | 0.10 | 0.00 | 0.00 | 0.00 | 0.25 | 0.00 | 0.03 | 0.00 | 0.05 | 0.00 | 0.00 | 0.00 | 0.19 | 0.00 |
| HPSE | ENSG00000173083 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.03 | 0.01 | 0.06 | 0.05 | 0.00 | 0.00 | 0.00 | 0.07 | 0.02 | 0.04 | 0.07 | 0.04 | 0.04 | 0.04 | 0.05 | 0.05 | 0.03 | 0.05 | 0.01 | 0.02 | 0.02 | 0.01 | 0.01 | 0.01 | 0.00 | 0.11 | 0.00 | 0.03 | 0.06 | 0.02 | 0.02 | 0.02 | 0.00 | 0.00 | 0.04 | 0.04 | 0.06 | 0.18 | 0.03 | 0.04 | 0.02 | 0.02 | 0.02 | 0.09 | 0.07 | 0.05 | 0.00 | 0.02 | 0.00 | 0.01 | 0.00 | 0.05 | 0.00 | 0.02 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.03 |
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