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 |
| HIPK3 | ENSG00000110422 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.04 | 0.13 | 0.04 | 0.00 | 0.00 | 0.00 | 0.04 | 0.05 | 0.02 | 0.13 | 0.01 | 0.08 | 0.01 | 0.23 | 0.03 | 0.08 | 0.01 | 0.01 | 0.00 | 0.01 | 0.00 | 0.01 | 0.02 | 0.01 | 0.00 | 0.00 | 0.05 | 0.02 | 0.01 | 0.02 | 0.04 | 0.00 | 0.00 | 0.18 | 0.01 | 0.23 | 0.06 | 0.06 | 0.00 | 0.03 | 0.02 | 0.01 | 0.05 | 0.07 | 0.09 | 0.00 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.01 | 0.03 | 0.01 | 0.00 | 0.00 | 0.04 | 0.02 |
| TEK | ENSG00000120156 | 0.00 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.03 | 0.05 | 0.10 | 0.00 | 0.02 | 0.01 | 0.57 | 0.05 | 0.09 | 0.18 | 0.17 | 0.04 | 0.08 | 0.10 | 0.12 | 0.03 | 0.10 | 0.02 | 0.01 | 0.01 | 0.03 | 0.04 | 0.11 | 0.02 | 0.03 | 0.00 | 0.01 | 0.01 | 0.10 | 0.01 | 0.00 | 0.00 | 0.00 | 0.05 | 0.06 | 0.09 | 0.11 | 0.01 | 0.04 | 0.03 | 0.02 | 0.03 | 0.11 | 0.14 | 0.13 | 0.02 | 0.00 | 0.00 | 0.00 | 0.04 | 0.00 | 0.01 | 0.10 | 0.02 | 0.39 | 0.00 | 0.00 | 0.04 | 0.13 |
| PHKG1 | ENSG00000164776 | 0.00 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.22 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.18 | 0.01 | 0.34 | 0.02 | 0.47 | 0.01 | 0.37 | 0.02 | 0.12 | 0.01 | 0.03 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.06 | 0.01 | 0.07 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.11 | 0.02 | 0.09 | 0.04 | 0.08 | 0.00 | 0.05 | 0.01 | 0.01 | 0.00 | 0.08 | 0.05 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.12 | 0.00 | 0.56 | 0.01 | 0.03 | 0.00 | 0.05 | 0.03 |
| CYP2C18 | ENSG00000108242 | 0.00 | 0.02 | 0.00 | 0.01 | 0.00 | 0.05 | 0.01 | 0.11 | 0.03 | 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 | 0.02 | 0.10 | 0.00 | 0.10 | 0.00 | 0.06 | 0.01 | 0.03 | 0.02 | 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 |
| NEK3 | ENSG00000136098 | 0.00 | 0.02 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.35 | 0.03 | 0.23 | 0.00 | 0.00 | 0.00 | 0.14 | 0.03 | 0.07 | 0.02 | 0.10 | 0.01 | 0.11 | 0.12 | 0.05 | 0.12 | 0.04 | 0.10 | 0.02 | 0.11 | 0.04 | 0.01 | 0.01 | 0.02 | 0.26 | 0.00 | 0.03 | 0.00 | 0.07 | 0.00 | 0.00 | 0.00 | 0.02 | 0.02 | 0.12 | 0.06 | 0.22 | 0.02 | 0.20 | 0.01 | 0.03 | 0.03 | 0.12 | 0.01 | 0.34 | 0.03 | 0.02 | 0.00 | 0.00 | 0.03 | 0.06 | 0.00 | 0.09 | 0.01 | 0.16 | 0.00 | 0.00 | 0.03 | 0.04 |
| EPHB1 | ENSG00000154928 | 0.02 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.08 | 0.01 | 0.06 | 0.02 | 0.00 | 0.01 | 0.00 | 0.05 | 0.05 | 0.01 | 0.24 | 0.01 | 0.19 | 0.00 | 0.23 | 0.03 | 0.09 | 0.02 | 0.01 | 0.01 | 0.02 | 0.01 | 0.00 | 0.01 | 0.05 | 0.01 | 0.00 | 0.03 | 0.06 | 0.02 | 0.00 | 0.06 | 0.00 | 0.00 | 0.07 | 0.02 | 0.40 | 0.03 | 0.22 | 0.01 | 0.08 | 0.01 | 0.19 | 0.02 | 0.03 | 0.06 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.02 | 0.01 | 0.02 | 0.02 | 0.04 | 0.00 | 0.00 | 0.01 | 0.05 |
| ADCK1 | ENSG00000063761 | 0.01 | 0.02 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.04 | 0.05 | 0.04 | 0.00 | 0.00 | 0.00 | 0.06 | 0.04 | 0.05 | 0.06 | 0.03 | 0.05 | 0.02 | 0.07 | 0.03 | 0.02 | 0.04 | 0.00 | 0.03 | 0.01 | 0.03 | 0.01 | 0.01 | 0.00 | 0.09 | 0.00 | 0.31 | 0.01 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.02 | 0.10 | 0.15 | 0.16 | 0.06 | 0.05 | 0.04 | 0.01 | 0.06 | 0.06 | 0.08 | 0.13 | 0.03 | 0.01 | 0.00 | 0.00 | 0.04 | 0.00 | 0.00 | 0.11 | 0.01 | 0.07 | 0.03 | 0.00 | 0.00 | 0.04 |
| CEP41 | ENSG00000106477 | 0.01 | 0.01 | 0.13 | 0.00 | 0.01 | 0.00 | 0.02 | 0.04 | 0.04 | 0.04 | 0.00 | 0.01 | 0.04 | 0.05 | 0.08 | 0.02 | 0.06 | 0.06 | 0.02 | 0.13 | 0.05 | 0.18 | 0.03 | 0.07 | 0.02 | 0.00 | 0.03 | 0.02 | 0.01 | 0.04 | 0.05 | 0.04 | 0.00 | 0.02 | 0.01 | 0.06 | 0.00 | 0.01 | 0.00 | 0.00 | 0.09 | 0.03 | 0.40 | 0.02 | 0.02 | 0.07 | 0.07 | 0.05 | 0.15 | 0.14 | 0.14 | 0.03 | 0.02 | 0.03 | 0.00 | 0.05 | 0.02 | 0.11 | 0.13 | 0.00 | 0.09 | 0.00 | 0.00 | 0.00 | 0.20 | 0.01 |
| MERTK | ENSG00000153208 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.05 | 0.06 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.01 | 0.08 | 0.02 | 0.07 | 0.01 | 0.20 | 0.02 | 0.07 | 0.02 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.01 | 0.02 | 0.04 | 0.00 | 0.07 | 0.07 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.03 | 0.11 | 0.11 | 0.06 | 0.01 | 0.09 | 0.01 | 0.23 | 0.00 | 0.13 | 0.02 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.06 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.01 |
| LAMC3 | ENSG00000050555 | 0.00 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 | 0.05 | 0.03 | 0.00 | 0.01 | 0.00 | 0.02 | 0.04 | 0.03 | 0.06 | 0.02 | 0.08 | 0.02 | 0.12 | 0.03 | 0.11 | 0.01 | 0.02 | 0.01 | 0.04 | 0.04 | 0.00 | 0.00 | 0.05 | 0.03 | 0.06 | 0.01 | 0.10 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.06 | 0.08 | 0.24 | 0.07 | 0.01 | 0.04 | 0.05 | 0.08 | 0.11 | 0.05 | 0.10 | 0.03 | 0.03 | 0.01 | 0.00 | 0.05 | 0.00 | 0.02 | 0.01 | 0.04 | 0.02 | 0.00 | 0.03 | 0.02 | 0.03 |
| TLK2 | ENSG00000146872 | 0.02 | 0.00 | 0.06 | 0.00 | 0.00 | 0.00 | 0.04 | 0.01 | 0.26 | 0.00 | 0.02 | 0.00 | 0.12 | 0.00 | 0.13 | 0.01 | 0.18 | 0.01 | 0.07 | 0.02 | 0.24 | 0.02 | 0.16 | 0.01 | 0.06 | 0.01 | 0.07 | 0.05 | 0.07 | 0.09 | 0.20 | 0.01 | 0.12 | 0.01 | 0.21 | 0.03 | 0.02 | 0.01 | 0.00 | 0.00 | 0.60 | 0.01 | 0.28 | 0.04 | 0.19 | 0.02 | 0.09 | 0.03 | 0.22 | 0.03 | 0.23 | 0.02 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.06 | 0.00 | 0.03 | 0.01 | 0.16 | 0.00 | 0.24 | 0.01 |
| ANXA2 | ENSG00000182718 | 0.00 | 0.00 | 0.00 | 0.01 | 0.14 | 0.00 | 0.01 | 0.02 | 0.01 | 0.06 | 0.00 | 0.00 | 0.08 | 0.00 | 0.03 | 0.04 | 0.04 | 0.04 | 0.02 | 0.02 | 0.05 | 0.03 | 0.03 | 0.04 | 0.01 | 0.02 | 0.00 | 0.05 | 0.01 | 0.01 | 0.03 | 0.01 | 0.00 | 0.01 | 0.06 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.04 | 0.05 | 0.10 | 0.16 | 0.04 | 0.04 | 0.02 | 0.07 | 0.02 | 0.24 | 0.13 | 0.02 | 0.01 | 0.02 | 0.00 | 0.00 | 0.06 | 0.02 | 0.01 | 0.02 | 0.01 | 0.05 | 0.00 | 0.00 | 0.04 | 0.03 |
| SLC13A2 | ENSG00000007216 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.01 | 0.24 | 0.01 | 0.08 | 0.00 | 0.00 | 0.03 | 0.07 | 0.01 | 0.12 | 0.03 | 0.04 | 0.02 | 0.14 | 0.01 | 0.13 | 0.01 | 0.11 | 0.01 | 0.09 | 0.01 | 0.03 | 0.01 | 0.04 | 0.00 | 0.07 | 0.01 | 0.02 | 0.05 | 0.00 | 0.14 | 0.00 | 0.00 | 0.32 | 0.03 | 0.17 | 0.07 | 0.02 | 0.03 | 0.16 | 0.03 | 0.23 | 0.05 | 0.07 | 0.16 | 0.00 | 0.01 | 0.00 | 0.02 | 0.06 | 0.00 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.02 | 0.03 |
| SCN3A | ENSG00000153253 | 0.02 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.01 | 0.11 | 0.07 | 0.05 | 0.00 | 0.01 | 0.00 | 0.03 | 0.08 | 0.01 | 0.10 | 0.03 | 0.07 | 0.01 | 0.10 | 0.04 | 0.03 | 0.04 | 0.01 | 0.02 | 0.01 | 0.01 | 0.02 | 0.01 | 0.05 | 0.05 | 0.00 | 0.01 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.03 | 0.30 | 0.05 | 0.07 | 0.01 | 0.05 | 0.01 | 0.09 | 0.00 | 0.06 | 0.08 | 0.04 | 0.01 | 0.00 | 0.00 | 0.00 | 0.11 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.02 |
| IDO1 | ENSG00000131203 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.09 | 0.29 | 0.05 | 0.00 | 0.00 | 0.02 | 0.00 | 0.19 | 0.04 | 0.54 | 0.03 | 0.18 | 0.03 | 0.28 | 0.06 | 0.05 | 0.04 | 0.16 | 0.03 | 0.13 | 0.05 | 0.08 | 0.00 | 0.06 | 0.06 | 0.03 | 0.01 | 0.09 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.48 | 0.04 | 0.21 | 0.07 | 0.08 | 0.03 | 0.13 | 0.02 | 0.56 | 0.11 | 0.17 | 0.04 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.04 | 0.03 |
| ADCK5 | ENSG00000173137 | 0.02 | 0.00 | 0.02 | 0.01 | 0.06 | 0.00 | 0.05 | 0.03 | 0.19 | 0.03 | 0.02 | 0.00 | 0.10 | 0.05 | 0.25 | 0.02 | 0.36 | 0.02 | 0.28 | 0.01 | 0.42 | 0.02 | 0.20 | 0.02 | 0.15 | 0.03 | 0.25 | 0.03 | 0.13 | 0.01 | 0.35 | 0.01 | 0.25 | 0.01 | 0.10 | 0.00 | 0.01 | 0.03 | 0.00 | 0.01 | 0.41 | 0.04 | 1.46 | 0.05 | 0.20 | 0.01 | 0.12 | 0.02 | 0.18 | 0.03 | 0.16 | 0.11 | 0.06 | 0.03 | 0.02 | 0.00 | 0.26 | 0.02 | 0.17 | 0.05 | 0.03 | 0.03 | 0.48 | 0.00 | 0.23 | 0.02 |
| NGFR | ENSG00000064300 | 0.00 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.10 | 0.02 | 0.00 | 0.00 | 0.09 | 0.00 | 0.09 | 0.00 | 0.11 | 0.01 | 0.02 | 0.01 | 0.14 | 0.02 | 0.09 | 0.01 | 0.02 | 0.01 | 0.06 | 0.04 | 0.03 | 0.02 | 0.05 | 0.01 | 0.02 | 0.01 | 0.01 | 0.04 | 0.01 | 0.04 | 0.00 | 0.00 | 0.48 | 0.03 | 0.16 | 0.04 | 0.06 | 0.00 | 0.05 | 0.04 | 0.27 | 0.04 | 0.12 | 0.03 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.02 | 0.01 | 0.03 | 0.03 | 0.12 | 0.01 |
| SLC16A2 | ENSG00000147100 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.02 | 0.05 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.02 | 0.04 | 0.03 | 0.03 | 0.01 | 0.06 | 0.03 | 0.03 | 0.01 | 0.01 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.01 | 0.26 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.02 | 0.13 | 0.05 | 0.06 | 0.02 | 0.04 | 0.01 | 0.04 | 0.00 | 0.15 | 0.09 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.03 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 |
| FGG | ENSG00000171557 | 0.01 | 0.02 | 0.00 | 0.01 | 0.06 | 0.02 | 0.01 | 0.02 | 0.05 | 0.11 | 0.00 | 0.02 | 0.00 | 0.01 | 0.05 | 0.06 | 0.01 | 0.11 | 0.01 | 0.09 | 0.05 | 0.06 | 0.06 | 0.07 | 0.01 | 0.06 | 0.02 | 0.04 | 0.01 | 0.04 | 0.09 | 0.06 | 0.00 | 0.12 | 0.10 | 0.05 | 0.00 | 0.03 | 0.00 | 0.00 | 0.06 | 0.07 | 0.07 | 0.26 | 0.03 | 0.08 | 0.04 | 0.05 | 0.06 | 0.05 | 0.10 | 0.10 | 0.01 | 0.01 | 0.00 | 0.00 | 0.03 | 0.03 | 0.00 | 0.09 | 0.00 | 0.03 | 0.00 | 0.00 | 0.04 | 0.05 |
| CBX3 | ENSG00000122565 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.09 | 0.02 | 0.00 | 0.00 | 0.00 | 0.02 | 0.07 | 0.00 | 0.08 | 0.02 | 0.04 | 0.01 | 0.16 | 0.02 | 0.06 | 0.01 | 0.04 | 0.00 | 0.03 | 0.00 | 0.01 | 0.00 | 0.06 | 0.00 | 0.00 | 0.01 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.09 | 0.02 | 0.19 | 0.17 | 0.04 | 0.00 | 0.05 | 0.02 | 0.04 | 0.07 | 0.18 | 0.03 | 0.07 | 0.00 | 0.00 | 0.01 | 0.00 | 0.02 | 0.01 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.07 | 0.02 |
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