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 |
| LRRN3 | ENSG00000173114 | 0.01 | 0.02 | 0.05 | 0.01 | 0.01 | 0.00 | 0.02 | 0.04 | 0.05 | 0.04 | 0.00 | 0.01 | 0.03 | 0.02 | 0.11 | 0.04 | 0.09 | 0.07 | 0.10 | 0.12 | 0.24 | 0.51 | 0.08 | 0.27 | 0.01 | 0.07 | 0.01 | 0.11 | 0.01 | 0.05 | 0.09 | 0.03 | 0.00 | 0.05 | 0.02 | 0.06 | 0.00 | 0.04 | 0.00 | 0.00 | 0.05 | 0.04 | 0.27 | 0.12 | 0.03 | 0.08 | 0.04 | 0.08 | 0.05 | 0.16 | 0.16 | 0.05 | 0.05 | 0.02 | 0.00 | 0.04 | 0.09 | 0.10 | 0.09 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.11 | 0.04 |
| CYSLTR1 | ENSG00000173198 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.02 | 0.02 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.02 | 0.04 | 0.03 | 0.03 | 0.01 | 0.07 | 0.04 | 0.04 | 0.01 | 0.01 | 0.01 | 0.01 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.02 | 0.11 | 0.03 | 0.03 | 0.02 | 0.02 | 0.02 | 0.01 | 0.05 | 0.17 | 0.09 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 |
| PARP15 | ENSG00000173200 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.02 | 0.05 | 0.02 | 0.00 | 0.01 | 0.00 | 0.01 | 0.04 | 0.02 | 0.11 | 0.01 | 0.03 | 0.00 | 0.08 | 0.04 | 0.05 | 0.02 | 0.00 | 0.00 | 0.03 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 | 0.00 | 0.02 | 0.03 | 0.01 | 0.00 | 0.05 | 0.00 | 0.00 | 0.03 | 0.04 | 0.25 | 0.04 | 0.06 | 0.01 | 0.04 | 0.01 | 0.05 | 0.09 | 0.08 | 0.07 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.03 | 0.01 | 0.07 | 0.00 | 0.00 | 0.01 | 0.04 |
| ABCD2 | ENSG00000173208 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.08 | 0.03 | 0.00 | 0.00 | 0.01 | 0.01 | 0.09 | 0.03 | 0.04 | 0.02 | 0.02 | 0.04 | 0.04 | 0.06 | 0.07 | 0.04 | 0.01 | 0.02 | 0.02 | 0.03 | 0.05 | 0.04 | 0.02 | 0.01 | 0.00 | 0.01 | 0.11 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.05 | 0.03 | 0.22 | 0.03 | 0.05 | 0.00 | 0.05 | 0.00 | 0.20 | 0.05 | 0.19 | 0.10 | 0.09 | 0.00 | 0.00 | 0.00 | 0.04 | 0.00 | 0.03 | 0.04 | 0.01 | 0.03 | 0.00 | 0.00 | 0.05 | 0.05 |
| TUBB8P12 | ENSG00000173213 | 0.00 | 0.00 | 0.01 | 0.00 | 0.01 | 0.01 | 0.01 | 0.03 | 0.09 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.08 | 0.02 | 0.19 | 0.04 | 0.16 | 0.03 | 0.26 | 0.06 | 0.05 | 0.02 | 0.02 | 0.01 | 0.02 | 0.05 | 0.03 | 0.03 | 0.03 | 0.02 | 0.00 | 0.05 | 0.00 | 0.06 | 0.00 | 0.00 | 0.01 | 0.00 | 0.04 | 0.04 | 0.16 | 0.11 | 0.06 | 0.03 | 0.05 | 0.03 | 0.10 | 0.07 | 0.17 | 0.11 | 0.00 | 0.11 | 0.00 | 0.01 | 0.03 | 0.04 | 0.02 | 0.03 | 0.01 | 0.04 | 0.00 | 0.00 | 0.04 | 0.02 |
| KIAA1919 | ENSG00000173214 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.28 | 0.02 | 0.13 | 0.00 | 0.01 | 0.00 | 0.14 | 0.01 | 0.05 | 0.04 | 0.04 | 0.02 | 0.03 | 0.05 | 0.09 | 0.05 | 0.08 | 0.01 | 0.03 | 0.02 | 0.03 | 0.00 | 0.03 | 0.00 | 0.08 | 0.00 | 0.15 | 0.05 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.12 | 0.09 | 0.07 | 0.25 | 0.01 | 0.02 | 0.07 | 0.02 | 0.10 | 0.04 | 0.15 | 0.07 | 0.00 | 0.04 | 0.00 | 0.00 | 0.01 | 0.21 | 0.00 | 0.02 | 0.02 | 0.06 | 0.05 | 0.03 | 0.00 | 0.14 |
| LIPM | ENSG00000173239 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.30 | 0.03 | 0.13 | 0.00 | 0.02 | 0.01 | 0.14 | 0.01 | 0.05 | 0.02 | 0.12 | 0.01 | 0.09 | 0.03 | 0.12 | 0.01 | 0.13 | 0.01 | 0.09 | 0.00 | 0.08 | 0.01 | 0.04 | 0.02 | 0.07 | 0.20 | 0.07 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.01 | 0.01 | 0.11 | 0.07 | 0.31 | 0.01 | 0.12 | 0.04 | 0.12 | 0.09 | 0.12 | 0.01 | 0.16 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.27 | 0.00 | 0.04 | 0.00 | 0.15 | 0.00 | 0.00 | 0.00 | 0.06 |
| GPR151 | ENSG00000173250 | 0.31 | 0.00 | 0.02 | 0.01 | 0.02 | 0.00 | 0.03 | 0.02 | 0.02 | 0.05 | 0.00 | 0.00 | 0.02 | 0.06 | 0.04 | 0.03 | 0.01 | 0.03 | 0.01 | 0.05 | 0.02 | 0.04 | 0.02 | 0.05 | 0.01 | 0.02 | 0.02 | 0.01 | 0.02 | 0.02 | 0.08 | 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 | 0.06 | 0.04 | 0.00 | 0.00 | 0.00 | 0.10 | 0.04 | 0.00 | 0.00 | 0.05 | 0.02 | 0.02 | 0.00 | 0.03 | 0.02 | 0.14 |
| OR10K1 | ENSG00000173285 | 0.03 | 0.00 | 0.01 | 0.01 | 0.00 | 0.03 | 0.02 | 0.05 | 0.41 | 0.01 | 0.02 | 0.00 | 0.11 | 0.00 | 0.28 | 0.00 | 0.25 | 0.00 | 0.06 | 0.01 | 0.25 | 0.00 | 0.12 | 0.00 | 0.03 | 0.00 | 0.11 | 0.00 | 0.07 | 0.00 | 0.29 | 0.00 | 0.41 | 0.01 | 0.18 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.27 | 0.01 | 0.38 | 0.02 | 0.15 | 0.00 | 0.14 | 0.00 | 0.29 | 0.00 | 0.36 | 0.02 | 0.11 | 0.00 | 0.00 | 0.00 | 0.25 | 0.00 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.16 | 0.02 |
| GPR148 | ENSG00000173302 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.15 | 0.04 | 0.03 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 | 0.06 | 0.02 | 0.04 | 0.01 | 0.08 | 0.05 | 0.04 | 0.04 | 0.01 | 0.01 | 0.00 | 0.01 | 0.02 | 0.01 | 0.01 | 0.03 | 0.00 | 0.03 | 0.05 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.05 | 0.08 | 0.17 | 0.02 | 0.01 | 0.04 | 0.01 | 0.07 | 0.00 | 0.13 | 0.04 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.12 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 |
| MAP3K11 | ENSG00000173327 | 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 |
| CST9 | ENSG00000173335 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.02 | 0.05 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.09 | 0.02 | 0.05 | 0.03 | 0.04 | 0.02 | 0.08 | 0.03 | 0.05 | 0.01 | 0.05 | 0.01 | 0.03 | 0.02 | 0.04 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.04 | 0.03 | 0.08 | 0.05 | 0.04 | 0.02 | 0.03 | 0.01 | 0.05 | 0.00 | 0.10 | 0.01 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.00 | 0.03 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.02 |
| C1QB | ENSG00000173369 | 0.00 | 0.05 | 0.00 | 0.08 | 0.00 | 0.00 | 0.01 | 0.03 | 0.08 | 0.09 | 0.00 | 0.03 | 0.04 | 0.23 | 0.04 | 0.06 | 0.05 | 0.11 | 0.03 | 0.07 | 0.06 | 0.10 | 0.06 | 0.11 | 0.00 | 0.16 | 0.02 | 0.21 | 0.01 | 0.08 | 0.01 | 0.21 | 0.00 | 1.06 | 0.01 | 0.06 | 0.01 | 0.10 | 0.00 | 0.00 | 0.01 | 0.19 | 0.12 | 0.44 | 0.05 | 0.08 | 0.04 | 0.12 | 0.12 | 0.19 | 0.16 | 0.10 | 0.05 | 0.06 | 0.02 | 0.00 | 0.00 | 0.11 | 0.04 | 0.02 | 0.04 | 0.10 | 0.00 | 0.12 | 0.08 | 0.08 |
| C1QA | ENSG00000173372 | 0.00 | 0.05 | 0.00 | 0.08 | 0.00 | 0.00 | 0.01 | 0.03 | 0.08 | 0.09 | 0.00 | 0.03 | 0.04 | 0.23 | 0.04 | 0.06 | 0.05 | 0.11 | 0.03 | 0.07 | 0.06 | 0.10 | 0.06 | 0.11 | 0.00 | 0.16 | 0.02 | 0.21 | 0.01 | 0.08 | 0.01 | 0.21 | 0.00 | 1.06 | 0.01 | 0.06 | 0.01 | 0.10 | 0.00 | 0.00 | 0.01 | 0.19 | 0.12 | 0.44 | 0.04 | 0.08 | 0.04 | 0.12 | 0.12 | 0.19 | 0.16 | 0.10 | 0.05 | 0.06 | 0.02 | 0.00 | 0.00 | 0.11 | 0.04 | 0.02 | 0.04 | 0.11 | 0.00 | 0.12 | 0.08 | 0.08 |
| NDNF | ENSG00000173376 | 0.00 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.08 | 0.04 | 0.06 | 0.00 | 0.00 | 0.00 | 0.05 | 0.02 | 0.04 | 0.02 | 0.07 | 0.02 | 0.02 | 0.01 | 0.04 | 0.02 | 0.06 | 0.01 | 0.04 | 0.01 | 0.04 | 0.00 | 0.02 | 0.03 | 0.06 | 0.00 | 0.11 | 0.11 | 0.05 | 0.00 | 0.01 | 0.00 | 0.00 | 0.05 | 0.04 | 0.04 | 0.25 | 0.01 | 0.04 | 0.01 | 0.05 | 0.04 | 0.07 | 0.05 | 0.08 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.05 | 0.01 | 0.04 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.03 |
| OLR1 | ENSG00000173391 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.12 | 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 | 0.07 | 0.08 | 0.01 | 0.04 | 0.04 | 0.04 | 0.00 | 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 | 0.33 | 0.10 | 0.01 | 0.02 | 0.03 | 0.03 | 0.00 | 0.03 | 0.10 | 0.12 | 0.56 | 0.00 | 0.00 | 0.01 | 0.00 | 0.08 | 0.10 | 0.01 | 0.03 | 0.05 | 0.00 | 0.01 | 0.03 | 0.03 |
| RNASE8 | ENSG00000173431 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.02 | 0.09 | 0.06 | 0.00 | 0.00 | 0.00 | 0.05 | 0.15 | 0.03 | 0.14 | 0.08 | 0.10 | 0.06 | 0.09 | 0.07 | 0.09 | 0.04 | 0.03 | 0.02 | 0.01 | 0.08 | 0.01 | 0.05 | 0.09 | 0.00 | 0.00 | 0.02 | 0.28 | 0.03 | 0.01 | 0.02 | 0.00 | 0.00 | 0.08 | 0.03 | 0.45 | 0.10 | 0.07 | 0.01 | 0.09 | 0.03 | 0.16 | 0.08 | 0.18 | 0.09 | 0.02 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.03 | 0.03 | 0.10 | 0.00 | 0.00 | 0.03 | 0.02 |
| SAA1 | ENSG00000173432 | 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 | 0.00 | 0.03 | 0.03 | 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 |
| AGR3 | ENSG00000173467 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.02 | 0.25 | 0.01 | 0.00 | 0.00 | 0.08 | 0.00 | 0.11 | 0.01 | 0.11 | 0.01 | 0.08 | 0.01 | 0.20 | 0.02 | 0.11 | 0.01 | 0.05 | 0.00 | 0.03 | 0.00 | 0.01 | 0.00 | 0.06 | 0.00 | 0.00 | 0.01 | 0.11 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.08 | 0.04 | 0.12 | 0.29 | 0.03 | 0.01 | 0.08 | 0.03 | 0.12 | 0.03 | 0.14 | 0.03 | 0.09 | 0.00 | 0.00 | 0.02 | 0.03 | 0.06 | 0.00 | 0.01 | 0.05 | 0.01 | 0.00 | 0.00 | 0.12 | 0.02 |
| FKBP2 | ENSG00000173486 | 0.01 | 0.00 | 0.00 | 0.01 | 0.07 | 0.00 | 0.03 | 0.01 | 0.12 | 0.01 | 0.00 | 0.00 | 0.08 | 0.00 | 0.06 | 0.03 | 0.08 | 0.02 | 0.19 | 0.03 | 0.11 | 0.05 | 0.02 | 0.03 | 0.01 | 0.01 | 0.02 | 0.03 | 0.00 | 0.03 | 0.02 | 0.03 | 0.13 | 0.07 | 0.07 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.09 | 0.09 | 0.15 | 0.05 | 0.08 | 0.01 | 0.10 | 0.03 | 0.55 | 0.08 | 0.07 | 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 | 0.06 | 0.05 |
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