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 |
| HMGCS2 | ENSG00000134240 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.03 | 0.02 | 0.20 | 0.03 | 0.00 | 0.00 | 0.01 | 0.14 | 0.04 | 0.12 | 0.12 | 0.15 | 0.05 | 0.16 | 0.15 | 0.10 | 0.07 | 0.05 | 0.02 | 0.04 | 0.04 | 0.03 | 0.17 | 0.01 | 0.03 | 0.04 | 0.05 | 0.01 | 0.10 | 0.03 | 0.04 | 0.26 | 0.00 | 0.00 | 0.13 | 0.05 | 0.23 | 0.10 | 0.07 | 0.06 | 0.04 | 0.02 | 0.13 | 0.06 | 0.12 | 0.11 | 0.05 | 0.03 | 0.00 | 0.00 | 0.03 | 0.02 | 0.00 | 0.02 | 0.00 | 0.03 | 0.00 | 0.03 | 0.36 | 0.06 |
| WNT2B | ENSG00000134245 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.04 | 0.05 | 0.05 | 0.00 | 0.00 | 0.00 | 0.33 | 0.01 | 0.14 | 0.02 | 0.15 | 0.00 | 0.15 | 0.05 | 0.13 | 0.05 | 0.08 | 0.01 | 0.08 | 0.05 | 0.08 | 0.00 | 0.02 | 0.01 | 0.04 | 0.00 | 0.14 | 0.02 | 0.05 | 0.00 | 0.25 | 0.00 | 0.00 | 0.03 | 0.10 | 0.16 | 0.14 | 0.01 | 0.09 | 0.02 | 0.03 | 0.07 | 0.09 | 0.04 | 0.11 | 0.03 | 0.04 | 0.00 | 0.01 | 0.00 | 0.05 | 0.00 | 0.01 | 0.01 | 0.03 | 0.03 | 0.03 | 0.08 | 0.10 |
| ADAM30 | ENSG00000134249 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.03 | 0.02 | 0.21 | 0.03 | 0.00 | 0.00 | 0.01 | 0.14 | 0.04 | 0.12 | 0.14 | 0.13 | 0.07 | 0.16 | 0.16 | 0.10 | 0.07 | 0.04 | 0.02 | 0.04 | 0.04 | 0.02 | 0.18 | 0.01 | 0.03 | 0.03 | 0.05 | 0.01 | 0.10 | 0.03 | 0.04 | 0.26 | 0.00 | 0.00 | 0.14 | 0.05 | 0.23 | 0.09 | 0.07 | 0.06 | 0.04 | 0.02 | 0.13 | 0.04 | 0.13 | 0.11 | 0.06 | 0.03 | 0.00 | 0.00 | 0.03 | 0.02 | 0.00 | 0.01 | 0.01 | 0.03 | 0.00 | 0.03 | 0.36 | 0.05 |
| NGF | ENSG00000134259 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.05 | 0.09 | 0.05 | 0.00 | 0.00 | 0.00 | 0.30 | 0.02 | 0.14 | 0.02 | 0.17 | 0.00 | 0.15 | 0.09 | 0.16 | 0.04 | 0.08 | 0.00 | 0.06 | 0.00 | 0.06 | 0.06 | 0.02 | 0.02 | 0.04 | 0.00 | 0.15 | 0.02 | 0.05 | 0.03 | 0.25 | 0.00 | 0.00 | 0.04 | 0.08 | 0.18 | 0.13 | 0.01 | 0.08 | 0.02 | 0.03 | 0.03 | 0.06 | 0.04 | 0.11 | 0.03 | 0.03 | 0.00 | 0.00 | 0.03 | 0.09 | 0.00 | 0.01 | 0.02 | 0.03 | 0.00 | 0.03 | 0.13 | 0.09 |
| FKBP11 | ENSG00000134285 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.04 | 0.00 | 0.00 | 0.00 | 0.04 | 0.07 | 0.01 | 0.03 | 0.02 | 0.01 | 0.04 | 0.07 | 0.05 | 0.05 | 0.04 | 0.02 | 0.00 | 0.02 | 0.02 | 0.00 | 0.05 | 0.03 | 0.01 | 0.09 | 0.01 | 0.16 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.04 | 0.05 | 0.08 | 0.06 | 0.02 | 0.01 | 0.04 | 0.01 | 0.09 | 0.13 | 0.07 | 0.09 | 0.02 | 0.00 | 0.00 | 0.01 | 0.10 | 0.06 | 0.01 | 0.04 | 0.03 | 0.05 | 0.00 | 0.00 | 0.06 | 0.04 |
| LDHA | ENSG00000134333 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.03 | 0.01 | 0.01 | 0.01 | 0.07 | 0.00 | 0.00 | 0.02 | 0.03 | 0.02 | 0.04 | 0.06 | 0.07 | 0.01 | 0.04 | 0.04 | 0.03 | 0.03 | 0.02 | 0.02 | 0.00 | 0.01 | 0.01 | 0.00 | 0.02 | 0.04 | 0.01 | 0.00 | 0.03 | 0.03 | 0.02 | 0.06 | 0.04 | 0.00 | 0.00 | 0.07 | 0.05 | 0.06 | 0.24 | 0.01 | 0.04 | 0.03 | 0.03 | 0.01 | 0.04 | 0.09 | 0.07 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.01 | 0.01 | 0.00 | 0.00 | 0.03 | 0.01 |
| SAA2 | ENSG00000134339 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.03 | 0.01 | 0.01 | 0.01 | 0.07 | 0.00 | 0.00 | 0.02 | 0.03 | 0.02 | 0.04 | 0.06 | 0.07 | 0.01 | 0.04 | 0.04 | 0.03 | 0.02 | 0.02 | 0.02 | 0.00 | 0.01 | 0.01 | 0.00 | 0.02 | 0.04 | 0.02 | 0.03 | 0.01 | 0.00 | 0.02 | 0.06 | 0.04 | 0.00 | 0.00 | 0.06 | 0.05 | 0.05 | 0.24 | 0.01 | 0.04 | 0.03 | 0.03 | 0.01 | 0.04 | 0.09 | 0.07 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 |
| FST | ENSG00000134363 | 0.00 | 0.00 | 0.00 | 0.01 | 0.03 | 0.00 | 0.01 | 0.15 | 0.04 | 0.10 | 0.00 | 0.00 | 0.01 | 0.01 | 0.06 | 0.07 | 0.05 | 0.09 | 0.02 | 0.08 | 0.04 | 0.12 | 0.04 | 0.10 | 0.01 | 0.05 | 0.01 | 0.05 | 0.00 | 0.05 | 0.03 | 0.02 | 0.00 | 0.10 | 0.11 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.03 | 0.08 | 0.10 | 0.41 | 0.03 | 0.07 | 0.03 | 0.11 | 0.04 | 0.31 | 0.08 | 0.05 | 0.00 | 0.02 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.02 |
| CFHR4 | ENSG00000134365 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.03 | 0.14 | 0.05 | 0.02 | 0.00 | 0.10 | 0.00 | 0.10 | 0.01 | 0.09 | 0.01 | 0.05 | 0.01 | 0.11 | 0.07 | 0.05 | 0.02 | 0.04 | 0.00 | 0.11 | 0.02 | 0.01 | 0.00 | 0.21 | 0.01 | 0.20 | 0.02 | 0.04 | 0.03 | 0.01 | 0.00 | 0.00 | 0.00 | 0.18 | 0.01 | 0.27 | 0.06 | 0.07 | 0.00 | 0.07 | 0.01 | 0.07 | 0.03 | 0.12 | 0.11 | 0.06 | 0.00 | 0.01 | 0.01 | 0.26 | 0.02 | 0.00 | 0.01 | 0.03 | 0.02 | 0.06 | 0.00 | 0.17 | 0.03 |
| CFHR5 | ENSG00000134389 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.03 | 0.14 | 0.05 | 0.02 | 0.00 | 0.10 | 0.00 | 0.10 | 0.01 | 0.09 | 0.01 | 0.05 | 0.01 | 0.11 | 0.07 | 0.05 | 0.02 | 0.04 | 0.00 | 0.11 | 0.02 | 0.01 | 0.00 | 0.21 | 0.01 | 0.20 | 0.02 | 0.04 | 0.03 | 0.01 | 0.00 | 0.00 | 0.00 | 0.19 | 0.01 | 0.28 | 0.06 | 0.07 | 0.00 | 0.07 | 0.01 | 0.07 | 0.03 | 0.12 | 0.11 | 0.06 | 0.00 | 0.01 | 0.01 | 0.26 | 0.02 | 0.00 | 0.01 | 0.03 | 0.02 | 0.06 | 0.00 | 0.17 | 0.03 |
| ERN2 | ENSG00000134398 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.15 | 0.03 | 0.00 | 0.00 | 0.02 | 0.04 | 0.04 | 0.01 | 0.04 | 0.01 | 0.03 | 0.02 | 0.02 | 0.01 | 0.01 | 0.01 | 0.02 | 0.01 | 0.01 | 0.00 | 0.01 | 0.00 | 0.04 | 0.01 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.04 | 0.01 | 0.07 | 0.05 | 0.01 | 0.01 | 0.03 | 0.01 | 0.17 | 0.03 | 0.01 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.12 | 0.02 | 0.00 | 0.02 | 0.00 | 0.07 | 0.00 | 0.00 | 0.01 | 0.02 |
| GRP | ENSG00000134443 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.09 | 0.01 | 0.07 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.11 | 0.03 | 0.07 | 0.01 | 0.14 | 0.03 | 0.22 | 0.01 | 0.17 | 0.00 | 0.10 | 0.00 | 0.10 | 0.00 | 0.08 | 0.02 | 0.07 | 0.00 | 0.10 | 0.01 | 0.03 | 0.01 | 0.00 | 0.00 | 0.00 | 0.05 | 0.05 | 0.05 | 0.32 | 0.00 | 0.04 | 0.01 | 0.07 | 0.13 | 0.11 | 0.10 | 0.06 | 0.00 | 0.07 | 0.00 | 0.00 | 0.08 | 0.00 | 0.01 | 0.03 | 0.01 | 0.03 | 0.00 | 0.01 | 0.02 | 0.02 |
| IL15RA | ENSG00000134470 | 0.01 | 0.01 | 0.03 | 0.00 | 0.00 | 0.00 | 0.02 | 0.04 | 0.39 | 0.00 | 0.00 | 0.00 | 0.02 | 0.14 | 0.04 | 0.05 | 0.04 | 0.07 | 0.02 | 0.04 | 0.10 | 0.06 | 0.08 | 0.03 | 0.02 | 0.02 | 0.02 | 0.00 | 0.03 | 0.03 | 0.02 | 0.02 | 0.00 | 0.05 | 0.05 | 0.03 | 0.01 | 0.00 | 0.00 | 0.00 | 0.19 | 0.01 | 0.35 | 0.10 | 0.03 | 0.01 | 0.05 | 0.01 | 0.21 | 0.00 | 0.05 | 0.11 | 0.00 | 0.03 | 0.00 | 0.00 | 0.04 | 0.02 | 0.05 | 0.01 | 0.03 | 0.02 | 0.00 | 0.02 | 0.02 | 0.02 |
| CCNH | ENSG00000134480 | 0.01 | 0.01 | 0.01 | 0.01 | 0.05 | 0.01 | 0.00 | 0.13 | 0.01 | 0.09 | 0.00 | 0.01 | 0.00 | 0.04 | 0.01 | 0.08 | 0.00 | 0.11 | 0.00 | 0.08 | 0.01 | 0.15 | 0.00 | 0.14 | 0.00 | 0.09 | 0.01 | 0.03 | 0.00 | 0.07 | 0.02 | 0.05 | 0.00 | 0.08 | 0.06 | 0.03 | 0.01 | 0.05 | 0.00 | 0.00 | 0.01 | 0.08 | 0.04 | 0.64 | 0.00 | 0.06 | 0.00 | 0.08 | 0.00 | 0.21 | 0.03 | 0.05 | 0.00 | 0.00 | 0.00 | 0.05 | 0.00 | 0.00 | 0.01 | 0.02 | 0.01 | 0.01 | 0.00 | 0.00 | 0.06 | 0.04 |
| KLRD1 | ENSG00000134539 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.13 | 0.06 | 0.05 | 0.01 | 0.00 | 0.00 | 0.05 | 0.03 | 0.09 | 0.12 | 0.01 | 0.10 | 0.02 | 0.07 | 0.02 | 0.06 | 0.08 | 0.01 | 0.03 | 0.04 | 0.04 | 0.01 | 0.06 | 0.01 | 0.05 | 0.14 | 0.05 | 0.03 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.10 | 0.05 | 0.32 | 0.10 | 0.01 | 0.02 | 0.03 | 0.03 | 0.00 | 0.03 | 0.10 | 0.13 | 0.56 | 0.00 | 0.00 | 0.03 | 0.00 | 0.08 | 0.10 | 0.01 | 0.02 | 0.05 | 0.00 | 0.01 | 0.04 | 0.03 |
| KLRC1 | ENSG00000134545 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.03 | 0.01 | 0.13 | 0.06 | 0.05 | 0.01 | 0.00 | 0.00 | 0.05 | 0.03 | 0.09 | 0.12 | 0.01 | 0.10 | 0.02 | 0.05 | 0.02 | 0.05 | 0.08 | 0.01 | 0.03 | 0.04 | 0.04 | 0.01 | 0.06 | 0.01 | 0.05 | 0.14 | 0.05 | 0.03 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.10 | 0.05 | 0.31 | 0.10 | 0.01 | 0.02 | 0.03 | 0.03 | 0.03 | 0.03 | 0.11 | 0.12 | 0.56 | 0.00 | 0.00 | 0.03 | 0.00 | 0.08 | 0.10 | 0.01 | 0.02 | 0.05 | 0.00 | 0.01 | 0.05 | 0.03 |
| SPX | ENSG00000134548 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.02 | 0.06 | 0.06 | 0.04 | 0.01 | 0.00 | 0.02 | 0.04 | 0.18 | 0.04 | 0.17 | 0.01 | 0.08 | 0.01 | 0.15 | 0.01 | 0.13 | 0.03 | 0.02 | 0.01 | 0.07 | 0.03 | 0.08 | 0.04 | 0.01 | 0.03 | 0.14 | 0.03 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.08 | 0.04 | 0.32 | 0.06 | 0.01 | 0.01 | 0.05 | 0.01 | 0.17 | 0.03 | 0.14 | 0.09 | 0.63 | 0.00 | 0.00 | 0.01 | 0.00 | 0.04 | 0.08 | 0.01 | 0.04 | 0.02 | 0.00 | 0.00 | 0.05 | 0.01 |
| ACP2 | ENSG00000134575 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.00 | 0.00 | 0.09 | 0.03 | 0.04 | 0.00 | 0.00 | 0.00 | 0.01 | 0.04 | 0.02 | 0.10 | 0.03 | 0.06 | 0.01 | 0.08 | 0.05 | 0.06 | 0.01 | 0.00 | 0.01 | 0.02 | 0.00 | 0.03 | 0.01 | 0.02 | 0.00 | 0.00 | 0.07 | 0.16 | 0.02 | 0.00 | 0.03 | 0.00 | 0.00 | 0.06 | 0.03 | 0.11 | 0.07 | 0.07 | 0.03 | 0.07 | 0.02 | 0.13 | 0.15 | 0.09 | 0.09 | 0.00 | 0.04 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.04 | 0.00 | 0.02 | 0.01 | 0.04 |
| STK26 | ENSG00000134602 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.04 | 0.04 | 0.05 | 0.00 | 0.05 | 0.04 | 0.09 | 0.01 | 0.09 | 0.02 | 0.05 | 0.01 | 0.10 | 0.02 | 0.13 | 0.01 | 0.03 | 0.00 | 0.05 | 0.02 | 0.01 | 0.00 | 0.09 | 0.03 | 0.00 | 0.01 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.02 | 0.21 | 0.06 | 0.09 | 0.01 | 0.02 | 0.02 | 0.04 | 0.10 | 0.03 | 0.14 | 0.00 | 0.02 | 0.01 | 0.00 | 0.07 | 0.09 | 0.01 | 0.02 | 0.01 | 0.02 | 0.00 | 0.00 | 0.02 | 0.03 |
| FOLH1B | ENSG00000134612 | 0.01 | 0.01 | 0.00 | 0.03 | 0.02 | 0.03 | 0.03 | 0.02 | 0.09 | 0.05 | 0.00 | 0.00 | 0.06 | 0.07 | 0.10 | 0.02 | 0.10 | 0.05 | 0.12 | 0.08 | 0.14 | 0.06 | 0.04 | 0.04 | 0.02 | 0.00 | 0.01 | 0.02 | 0.01 | 0.01 | 0.03 | 0.04 | 0.00 | 0.02 | 0.00 | 0.02 | 0.00 | 0.03 | 0.00 | 0.00 | 0.12 | 0.10 | 0.37 | 0.07 | 0.13 | 0.06 | 0.07 | 0.04 | 0.06 | 0.19 | 0.06 | 0.12 | 0.04 | 0.07 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.07 | 0.07 |
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