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 |
| TNFRSF8 | ENSG00000120949 | 0.00 | 0.06 | 0.01 | 0.08 | 0.00 | 0.00 | 0.00 | 0.05 | 0.10 | 0.07 | 0.00 | 0.02 | 0.04 | 0.26 | 0.06 | 0.05 | 0.05 | 0.11 | 0.04 | 0.08 | 0.16 | 0.08 | 0.11 | 0.08 | 0.01 | 0.13 | 0.00 | 0.20 | 0.03 | 0.06 | 0.03 | 0.22 | 0.00 | 1.07 | 0.04 | 0.14 | 0.01 | 0.09 | 0.00 | 0.00 | 0.02 | 0.19 | 0.21 | 0.36 | 0.06 | 0.10 | 0.07 | 0.10 | 0.08 | 0.23 | 0.19 | 0.19 | 0.08 | 0.09 | 0.02 | 0.00 | 0.00 | 0.03 | 0.00 | 0.03 | 0.07 | 0.11 | 0.00 | 0.07 | 0.06 | 0.11 |
| HYAL3 | ENSG00000186792 | 0.00 | 0.18 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.02 | 0.03 | 0.17 | 0.02 | 0.00 | 0.00 | 0.55 | 0.01 | 0.06 | 0.00 | 0.11 | 0.00 | 0.06 | 0.03 | 0.14 | 0.01 | 0.11 | 0.00 | 0.05 | 0.01 | 0.06 | 0.00 | 0.04 | 0.05 | 0.06 | 0.00 | 0.20 | 0.01 | 0.02 | 0.01 | 0.02 | 0.00 | 0.00 | 0.01 | 0.17 | 0.06 | 0.19 | 0.01 | 0.06 | 0.09 | 0.06 | 0.10 | 0.36 | 0.03 | 0.17 | 0.02 | 0.03 | 0.00 | 0.01 | 0.00 | 0.06 | 0.01 | 0.06 | 0.01 | 0.04 | 0.00 | 0.03 | 0.01 | 0.04 |
| PRSS3 | ENSG00000010438 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.02 | 0.07 | 0.03 | 0.00 | 0.00 | 0.01 | 0.11 | 0.06 | 0.01 | 0.35 | 0.04 | 0.18 | 0.04 | 0.21 | 0.04 | 0.14 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.04 | 0.00 | 0.03 | 0.01 | 0.24 | 0.01 | 0.06 | 0.06 | 0.00 | 0.00 | 0.00 | 0.00 | 0.07 | 0.03 | 0.10 | 0.06 | 0.01 | 0.01 | 0.05 | 0.02 | 0.14 | 0.05 | 0.12 | 0.05 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.03 | 0.06 | 0.00 | 0.00 | 0.05 | 0.04 |
| OPN3 | ENSG00000054277 | 0.01 | 0.02 | 0.01 | 0.01 | 0.00 | 0.01 | 0.02 | 0.05 | 0.10 | 0.03 | 0.02 | 0.00 | 0.05 | 0.08 | 0.12 | 0.01 | 0.15 | 0.02 | 0.07 | 0.01 | 0.18 | 0.04 | 0.12 | 0.03 | 0.04 | 0.02 | 0.08 | 0.02 | 0.01 | 0.01 | 0.19 | 0.01 | 0.23 | 0.02 | 0.06 | 0.06 | 0.00 | 0.04 | 0.00 | 0.00 | 0.26 | 0.02 | 0.47 | 0.11 | 0.11 | 0.02 | 0.10 | 0.02 | 0.30 | 0.00 | 0.03 | 0.23 | 0.05 | 0.02 | 0.01 | 0.00 | 0.05 | 0.19 | 0.03 | 0.03 | 0.03 | 0.05 | 0.08 | 0.03 | 0.21 | 0.03 |
| ADAMTSL1 | ENSG00000178031 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.03 | 0.08 | 0.14 | 0.01 | 0.03 | 0.01 | 0.20 | 0.02 | 0.09 | 0.08 | 0.11 | 0.13 | 0.04 | 0.15 | 0.10 | 0.04 | 0.08 | 0.02 | 0.02 | 0.01 | 0.03 | 0.04 | 0.10 | 0.01 | 0.04 | 0.00 | 0.05 | 0.04 | 0.06 | 0.00 | 0.02 | 0.00 | 0.00 | 0.05 | 0.05 | 0.14 | 0.13 | 0.05 | 0.03 | 0.05 | 0.02 | 0.04 | 0.05 | 0.06 | 0.14 | 0.02 | 0.01 | 0.00 | 0.00 | 0.04 | 0.02 | 0.00 | 0.11 | 0.02 | 0.35 | 0.00 | 0.00 | 0.02 | 0.11 |
| CX3CL1 | ENSG00000006210 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.01 | 0.04 | 0.00 | 0.00 | 0.00 | 0.01 | 0.04 | 0.03 | 0.03 | 0.01 | 0.03 | 0.02 | 0.09 | 0.01 | 0.03 | 0.03 | 0.02 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.01 | 0.02 | 0.00 | 0.01 | 0.06 | 0.06 | 0.00 | 0.02 | 0.00 | 0.00 | 0.03 | 0.04 | 0.05 | 0.13 | 0.00 | 0.07 | 0.04 | 0.06 | 0.02 | 0.12 | 0.02 | 0.06 | 0.12 | 0.01 | 0.00 | 0.00 | 0.05 | 0.02 | 0.01 | 0.01 | 0.00 | 0.02 | 0.00 | 0.03 | 0.00 | 0.04 |
| MIPEP | ENSG00000027001 | 0.02 | 0.02 | 0.01 | 0.01 | 0.00 | 0.00 | 0.03 | 0.05 | 0.08 | 0.06 | 0.00 | 0.02 | 0.00 | 0.17 | 0.01 | 0.11 | 0.02 | 0.12 | 0.01 | 0.16 | 0.09 | 0.10 | 0.08 | 0.04 | 0.21 | 0.00 | 0.22 | 0.03 | 0.00 | 0.01 | 0.04 | 0.12 | 0.00 | 0.15 | 0.00 | 0.09 | 0.00 | 0.01 | 0.00 | 0.01 | 0.08 | 0.08 | 0.11 | 0.20 | 0.03 | 0.15 | 0.02 | 0.05 | 0.01 | 0.16 | 0.12 | 0.20 | 0.00 | 0.01 | 0.00 | 0.00 | 0.04 | 0.11 | 0.00 | 0.06 | 0.01 | 0.07 | 0.00 | 0.00 | 0.05 | 0.04 |
| SLC2A9 | ENSG00000109667 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.03 | 0.08 | 0.04 | 0.00 | 0.00 | 0.00 | 0.03 | 0.02 | 0.04 | 0.04 | 0.05 | 0.03 | 0.05 | 0.09 | 0.05 | 0.06 | 0.04 | 0.01 | 0.02 | 0.04 | 0.03 | 0.00 | 0.02 | 0.03 | 0.04 | 0.00 | 0.01 | 0.08 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.04 | 0.23 | 0.06 | 0.01 | 0.03 | 0.05 | 0.02 | 0.13 | 0.00 | 0.07 | 0.06 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.01 | 0.03 | 0.02 | 0.00 | 0.05 | 0.02 |
| ACE2 | ENSG00000130234 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.06 | 0.01 | 0.04 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.05 | 0.11 | 0.04 | 0.02 | 0.02 | 0.06 | 0.04 | 0.05 | 0.02 | 0.00 | 0.01 | 0.12 | 0.02 | 0.00 | 0.01 | 0.01 | 0.02 | 0.00 | 0.01 | 0.02 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.05 | 0.03 | 0.15 | 0.17 | 0.05 | 0.01 | 0.04 | 0.02 | 0.06 | 0.07 | 0.12 | 0.05 | 0.06 | 0.01 | 0.00 | 0.00 | 0.00 | 0.07 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.04 | 0.02 |
| UPP1 | ENSG00000183696 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.06 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.08 | 0.01 | 0.12 | 0.03 | 0.09 | 0.01 | 0.17 | 0.03 | 0.07 | 0.00 | 0.02 | 0.00 | 0.01 | 0.00 | 0.02 | 0.00 | 0.03 | 0.00 | 0.00 | 0.01 | 0.07 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.02 | 0.13 | 0.05 | 0.02 | 0.00 | 0.04 | 0.02 | 0.04 | 0.00 | 0.04 | 0.03 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.05 | 0.02 | 0.00 | 0.06 | 0.01 | 0.00 | 0.00 | 0.03 | 0.03 |
| PRKCE | ENSG00000171132 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.06 | 0.10 | 0.01 | 0.00 | 0.00 | 0.01 | 0.05 | 0.07 | 0.01 | 0.23 | 0.02 | 0.05 | 0.02 | 0.06 | 0.03 | 0.04 | 0.04 | 0.00 | 0.02 | 0.03 | 0.02 | 0.02 | 0.04 | 0.05 | 0.02 | 0.00 | 0.05 | 0.00 | 0.03 | 0.02 | 0.01 | 0.00 | 0.00 | 0.06 | 0.02 | 0.29 | 0.06 | 0.08 | 0.00 | 0.07 | 0.01 | 0.12 | 0.02 | 0.05 | 0.05 | 0.13 | 0.01 | 0.00 | 0.00 | 0.10 | 0.02 | 0.01 | 0.00 | 0.00 | 0.01 | 0.03 | 0.00 | 0.04 | 0.02 |
| TRIB3 | ENSG00000101255 | 0.01 | 0.00 | 0.01 | 0.00 | 0.03 | 0.01 | 0.01 | 0.02 | 0.03 | 0.02 | 0.00 | 0.00 | 0.00 | 0.05 | 0.04 | 0.05 | 0.14 | 0.03 | 0.03 | 0.03 | 0.10 | 0.03 | 0.05 | 0.02 | 0.04 | 0.05 | 0.09 | 0.09 | 0.03 | 0.03 | 0.05 | 0.01 | 0.04 | 0.03 | 0.00 | 0.10 | 0.00 | 0.02 | 0.00 | 0.00 | 0.05 | 0.08 | 0.33 | 0.10 | 0.03 | 0.03 | 0.07 | 0.03 | 0.11 | 0.10 | 0.08 | 0.09 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.01 | 0.02 | 0.02 | 0.00 | 0.04 | 0.04 |
| STK32A | ENSG00000169302 | 0.31 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.02 | 0.02 | 0.02 | 0.05 | 0.00 | 0.00 | 0.02 | 0.06 | 0.05 | 0.04 | 0.01 | 0.03 | 0.01 | 0.05 | 0.02 | 0.04 | 0.02 | 0.05 | 0.01 | 0.02 | 0.03 | 0.01 | 0.02 | 0.02 | 0.09 | 0.02 | 0.09 | 0.01 | 0.22 | 0.04 | 0.00 | 0.04 | 0.01 | 0.00 | 0.03 | 0.02 | 0.15 | 0.10 | 0.02 | 0.01 | 0.02 | 0.02 | 0.09 | 0.02 | 0.07 | 0.04 | 0.00 | 0.00 | 0.00 | 0.10 | 0.04 | 0.00 | 0.01 | 0.05 | 0.01 | 0.03 | 0.00 | 0.03 | 0.02 | 0.14 |
| PAK1 | ENSG00000149269 | 0.00 | 0.01 | 0.00 | 0.01 | 0.09 | 0.00 | 0.05 | 0.00 | 0.24 | 0.02 | 0.00 | 0.00 | 0.08 | 0.00 | 0.18 | 0.01 | 0.15 | 0.02 | 0.27 | 0.03 | 0.28 | 0.03 | 0.18 | 0.01 | 0.02 | 0.00 | 0.03 | 0.02 | 0.01 | 0.01 | 0.08 | 0.02 | 0.18 | 0.02 | 0.01 | 0.00 | 0.02 | 0.02 | 0.00 | 0.00 | 0.62 | 0.04 | 0.76 | 0.02 | 0.17 | 0.01 | 0.16 | 0.01 | 0.20 | 0.15 | 0.22 | 0.05 | 0.02 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.01 | 0.00 | 0.00 | 0.35 | 0.01 |
| SLC24A3 | ENSG00000185052 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.03 | 0.06 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.02 | 0.05 | 0.03 | 0.05 | 0.01 | 0.05 | 0.04 | 0.05 | 0.02 | 0.07 | 0.03 | 0.11 | 0.02 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.01 | 0.01 | 0.08 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.03 | 0.11 | 0.06 | 0.05 | 0.02 | 0.03 | 0.02 | 0.05 | 0.02 | 0.06 | 0.04 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.00 | 0.02 | 0.01 | 0.01 | 0.00 | 0.00 | 0.04 | 0.02 |
| CD276 | ENSG00000103855 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.02 | 0.01 | 0.03 | 0.05 | 0.02 | 0.00 | 0.00 | 0.09 | 0.00 | 0.04 | 0.02 | 0.05 | 0.01 | 0.02 | 0.02 | 0.07 | 0.03 | 0.05 | 0.03 | 0.02 | 0.01 | 0.03 | 0.03 | 0.03 | 0.01 | 0.04 | 0.03 | 0.00 | 0.01 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.09 | 0.03 | 0.16 | 0.12 | 0.12 | 0.01 | 0.03 | 0.04 | 0.22 | 0.03 | 0.05 | 0.11 | 0.01 | 0.01 | 0.00 | 0.00 | 0.06 | 0.00 | 0.01 | 0.01 | 0.01 | 0.02 | 0.00 | 0.00 | 0.16 | 0.01 |
| STK31 | ENSG00000196335 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.09 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.09 | 0.01 | 0.11 | 0.02 | 0.05 | 0.01 | 0.19 | 0.01 | 0.07 | 0.01 | 0.05 | 0.00 | 0.03 | 0.00 | 0.01 | 0.00 | 0.06 | 0.00 | 0.00 | 0.01 | 0.06 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.10 | 0.03 | 0.17 | 0.19 | 0.04 | 0.00 | 0.08 | 0.03 | 0.22 | 0.01 | 0.16 | 0.04 | 0.06 | 0.00 | 0.00 | 0.01 | 0.03 | 0.05 | 0.01 | 0.00 | 0.05 | 0.01 | 0.00 | 0.00 | 0.07 | 0.03 |
| PCSK5 | ENSG00000099139 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.02 | 0.02 | 0.05 | 0.00 | 0.01 | 0.05 | 0.05 | 0.01 | 0.05 | 0.05 | 0.06 | 0.00 | 0.03 | 0.08 | 0.06 | 0.03 | 0.05 | 0.01 | 0.01 | 0.02 | 0.01 | 0.00 | 0.00 | 0.01 | 0.02 | 0.00 | 0.15 | 0.04 | 0.00 | 0.01 | 0.03 | 0.00 | 0.00 | 0.03 | 0.04 | 0.10 | 0.15 | 0.01 | 0.03 | 0.02 | 0.04 | 0.07 | 0.16 | 0.14 | 0.01 | 0.02 | 0.03 | 0.00 | 0.02 | 0.05 | 0.09 | 0.00 | 0.01 | 0.01 | 0.03 | 0.00 | 0.00 | 0.02 | 0.03 |
| PDGFRL | ENSG00000104213 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.18 | 0.00 | 0.14 | 0.00 | 0.00 | 0.02 | 0.03 | 0.02 | 0.07 | 0.01 | 0.10 | 0.00 | 0.07 | 0.07 | 0.05 | 0.11 | 0.04 | 0.00 | 0.11 | 0.00 | 0.18 | 0.01 | 0.05 | 0.01 | 0.12 | 0.00 | 0.05 | 0.00 | 0.00 | 0.01 | 0.02 | 0.00 | 0.00 | 0.03 | 0.14 | 0.05 | 0.39 | 0.00 | 0.05 | 0.02 | 0.08 | 0.16 | 0.18 | 0.04 | 0.04 | 0.05 | 0.01 | 0.00 | 0.00 | 0.00 | 0.11 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.01 | 0.02 | 0.04 |
| LCAT | ENSG00000213398 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.06 | 0.01 | 0.07 | 0.17 | 0.02 | 0.00 | 0.00 | 0.01 | 0.07 | 0.04 | 0.03 | 0.06 | 0.01 | 0.03 | 0.01 | 0.13 | 0.01 | 0.04 | 0.04 | 0.00 | 0.01 | 0.01 | 0.01 | 0.01 | 0.00 | 0.02 | 0.04 | 0.05 | 0.01 | 0.23 | 0.03 | 0.01 | 0.02 | 0.00 | 0.01 | 0.02 | 0.05 | 0.03 | 0.33 | 0.04 | 0.02 | 0.03 | 0.08 | 0.06 | 0.14 | 0.02 | 0.04 | 0.15 | 0.01 | 0.00 | 0.05 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.03 | 0.05 | 0.01 |
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