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 |
| ATAD2B | ENSG00000119778 | 0.00 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 | 0.09 | 0.01 | 0.00 | 0.00 | 0.03 | 0.08 | 0.06 | 0.01 | 0.08 | 0.03 | 0.03 | 0.02 | 0.06 | 0.06 | 0.03 | 0.03 | 0.01 | 0.00 | 0.01 | 0.02 | 0.01 | 0.04 | 0.08 | 0.02 | 0.00 | 0.05 | 0.01 | 0.06 | 0.01 | 0.00 | 0.00 | 0.00 | 0.05 | 0.04 | 0.18 | 0.13 | 0.08 | 0.00 | 0.12 | 0.03 | 0.26 | 0.03 | 0.06 | 0.10 | 0.17 | 0.01 | 0.00 | 0.00 | 0.02 | 0.03 | 0.01 | 0.01 | 0.02 | 0.03 | 0.05 | 0.00 | 0.03 | 0.04 |
| ABCG1 | ENSG00000160179 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.05 | 0.06 | 0.04 | 0.00 | 0.03 | 0.00 | 0.00 | 0.02 | 0.02 | 0.02 | 0.08 | 0.01 | 0.05 | 0.03 | 0.09 | 0.04 | 0.07 | 0.01 | 0.01 | 0.01 | 0.05 | 0.01 | 0.01 | 0.02 | 0.02 | 0.07 | 0.03 | 0.01 | 0.05 | 0.01 | 0.00 | 0.00 | 0.00 | 0.09 | 0.02 | 0.13 | 0.17 | 0.03 | 0.04 | 0.05 | 0.02 | 0.04 | 0.03 | 0.11 | 0.06 | 0.04 | 0.00 | 0.12 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.03 | 0.00 | 0.01 | 0.02 |
| KCNJ5 | ENSG00000120457 | 0.00 | 0.02 | 0.00 | 0.05 | 0.00 | 0.03 | 0.02 | 0.05 | 0.04 | 0.12 | 0.00 | 0.00 | 0.11 | 0.06 | 0.07 | 0.10 | 0.04 | 0.13 | 0.04 | 0.14 | 0.10 | 0.13 | 0.05 | 0.07 | 0.01 | 0.01 | 0.01 | 0.02 | 0.02 | 0.02 | 0.02 | 0.09 | 0.00 | 0.23 | 0.02 | 0.10 | 0.00 | 0.05 | 0.00 | 0.00 | 0.04 | 0.21 | 0.26 | 0.19 | 0.05 | 0.31 | 0.05 | 0.08 | 0.09 | 0.22 | 0.03 | 0.26 | 0.00 | 0.28 | 0.04 | 0.00 | 0.13 | 0.00 | 0.06 | 0.01 | 0.01 | 0.01 | 0.00 | 0.10 | 0.01 | 0.28 |
| HRH2 | ENSG00000113749 | 0.33 | 0.00 | 0.05 | 0.01 | 0.00 | 0.00 | 0.04 | 0.00 | 0.02 | 0.11 | 0.00 | 0.00 | 0.03 | 0.05 | 0.08 | 0.04 | 0.02 | 0.07 | 0.03 | 0.05 | 0.10 | 0.01 | 0.04 | 0.03 | 0.02 | 0.03 | 0.04 | 0.05 | 0.02 | 0.02 | 0.13 | 0.02 | 0.05 | 0.01 | 0.36 | 0.02 | 0.00 | 0.03 | 0.01 | 0.00 | 0.09 | 0.04 | 0.24 | 0.14 | 0.03 | 0.05 | 0.06 | 0.02 | 0.21 | 0.01 | 0.13 | 0.08 | 0.00 | 0.02 | 0.00 | 0.02 | 0.02 | 0.00 | 0.01 | 0.06 | 0.02 | 0.06 | 0.04 | 0.00 | 0.05 | 0.10 |
| ABCC6 | ENSG00000091262 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.11 | 0.06 | 0.00 | 0.00 | 0.03 | 0.02 | 0.03 | 0.02 | 0.05 | 0.03 | 0.03 | 0.02 | 0.04 | 0.03 | 0.05 | 0.02 | 0.02 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.05 | 0.02 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.05 | 0.02 | 0.19 | 0.07 | 0.09 | 0.00 | 0.05 | 0.01 | 0.16 | 0.00 | 0.08 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.09 | 0.00 | 0.01 | 0.01 | 0.01 | 0.02 | 0.00 | 0.00 | 0.04 | 0.01 |
| GABRP | ENSG00000094755 | 0.33 | 0.00 | 0.05 | 0.01 | 0.00 | 0.00 | 0.04 | 0.00 | 0.01 | 0.11 | 0.00 | 0.00 | 0.02 | 0.06 | 0.11 | 0.04 | 0.02 | 0.05 | 0.02 | 0.05 | 0.07 | 0.03 | 0.05 | 0.04 | 0.01 | 0.02 | 0.04 | 0.06 | 0.02 | 0.02 | 0.12 | 0.03 | 0.10 | 0.01 | 0.37 | 0.02 | 0.00 | 0.03 | 0.01 | 0.00 | 0.08 | 0.04 | 0.20 | 0.13 | 0.03 | 0.02 | 0.06 | 0.02 | 0.16 | 0.01 | 0.14 | 0.08 | 0.00 | 0.00 | 0.00 | 0.03 | 0.02 | 0.00 | 0.01 | 0.07 | 0.02 | 0.05 | 0.04 | 0.00 | 0.06 | 0.10 |
| NTF3 | ENSG00000185652 | 0.01 | 0.00 | 0.00 | 0.01 | 0.02 | 0.00 | 0.02 | 0.06 | 0.10 | 0.03 | 0.01 | 0.00 | 0.00 | 0.09 | 0.05 | 0.07 | 0.19 | 0.01 | 0.13 | 0.01 | 0.11 | 0.03 | 0.05 | 0.06 | 0.09 | 0.02 | 0.06 | 0.02 | 0.06 | 0.06 | 0.02 | 0.04 | 0.14 | 0.05 | 0.03 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.11 | 0.04 | 0.34 | 0.08 | 0.04 | 0.02 | 0.07 | 0.02 | 0.17 | 0.05 | 0.13 | 0.12 | 0.58 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.15 | 0.00 | 0.07 | 0.02 | 0.00 | 0.01 | 0.04 | 0.04 |
| IL1RAP | ENSG00000196083 | 0.05 | 0.00 | 0.03 | 0.01 | 0.00 | 0.01 | 0.03 | 0.05 | 0.16 | 0.01 | 0.00 | 0.00 | 0.00 | 0.07 | 0.14 | 0.06 | 1.43 | 0.01 | 0.58 | 0.00 | 0.74 | 0.02 | 0.24 | 0.02 | 0.05 | 0.01 | 0.06 | 0.02 | 0.03 | 0.00 | 0.12 | 0.03 | 0.12 | 0.03 | 0.10 | 0.00 | 0.00 | 0.10 | 0.00 | 0.00 | 0.19 | 0.02 | 0.95 | 0.07 | 0.63 | 0.00 | 0.34 | 0.01 | 0.79 | 0.11 | 0.13 | 0.09 | 0.23 | 0.00 | 0.00 | 0.00 | 0.07 | 0.04 | 0.02 | 0.05 | 0.09 | 0.07 | 0.00 | 0.00 | 0.03 | 0.04 |
| NAALAD2 | ENSG00000077616 | 0.01 | 0.01 | 0.00 | 0.03 | 0.02 | 0.03 | 0.02 | 0.01 | 0.09 | 0.05 | 0.00 | 0.00 | 0.06 | 0.06 | 0.10 | 0.03 | 0.11 | 0.05 | 0.12 | 0.08 | 0.14 | 0.04 | 0.03 | 0.03 | 0.02 | 0.00 | 0.01 | 0.02 | 0.01 | 0.01 | 0.03 | 0.04 | 0.00 | 0.02 | 0.00 | 0.02 | 0.01 | 0.03 | 0.00 | 0.00 | 0.11 | 0.10 | 0.37 | 0.08 | 0.13 | 0.07 | 0.06 | 0.04 | 0.06 | 0.19 | 0.06 | 0.11 | 0.04 | 0.07 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.09 | 0.07 |
| TYK2 | ENSG00000105397 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.02 | 0.10 | 0.04 | 0.00 | 0.01 | 0.09 | 0.01 | 0.02 | 0.05 | 0.08 | 0.06 | 0.05 | 0.04 | 0.06 | 0.06 | 0.05 | 0.04 | 0.02 | 0.01 | 0.02 | 0.04 | 0.01 | 0.03 | 0.04 | 0.12 | 0.00 | 0.01 | 0.13 | 0.03 | 0.00 | 0.00 | 0.00 | 0.01 | 0.11 | 0.04 | 0.60 | 0.20 | 0.12 | 0.05 | 0.24 | 0.08 | 0.72 | 0.18 | 0.27 | 0.02 | 0.02 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.05 | 0.01 | 0.02 | 0.02 | 0.02 | 0.02 |
| TUBD1 | ENSG00000108423 | 0.02 | 0.00 | 0.05 | 0.00 | 0.00 | 0.00 | 0.03 | 0.03 | 0.25 | 0.01 | 0.02 | 0.00 | 0.11 | 0.00 | 0.23 | 0.01 | 0.22 | 0.02 | 0.06 | 0.01 | 0.26 | 0.03 | 0.17 | 0.01 | 0.10 | 0.01 | 0.11 | 0.03 | 0.05 | 0.12 | 0.23 | 0.00 | 0.12 | 0.01 | 0.08 | 0.03 | 0.02 | 0.00 | 0.00 | 0.00 | 0.73 | 0.01 | 0.25 | 0.02 | 0.12 | 0.02 | 0.15 | 0.03 | 0.64 | 0.00 | 0.20 | 0.05 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.06 | 0.00 | 0.03 | 0.01 | 0.16 | 0.00 | 0.22 | 0.01 |
| CHRD | ENSG00000090539 | 0.05 | 0.00 | 0.03 | 0.01 | 0.00 | 0.01 | 0.03 | 0.03 | 0.17 | 0.00 | 0.00 | 0.00 | 0.00 | 0.08 | 0.15 | 0.05 | 1.85 | 0.00 | 0.65 | 0.00 | 0.72 | 0.02 | 0.23 | 0.01 | 0.04 | 0.00 | 0.06 | 0.03 | 0.03 | 0.01 | 0.11 | 0.02 | 0.12 | 0.01 | 0.10 | 0.00 | 0.00 | 0.10 | 0.00 | 0.00 | 0.18 | 0.02 | 1.12 | 0.02 | 0.62 | 0.00 | 0.34 | 0.01 | 0.76 | 0.09 | 0.12 | 0.10 | 0.22 | 0.00 | 0.00 | 0.01 | 0.06 | 0.00 | 0.06 | 0.00 | 0.20 | 0.02 | 0.00 | 0.00 | 0.03 | 0.05 |
| PTGER1 | ENSG00000160951 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.02 | 0.04 | 0.02 | 0.00 | 0.06 | 0.02 | 0.00 | 0.04 | 0.13 | 0.04 | 0.05 | 0.01 | 0.11 | 0.04 | 0.05 | 0.01 | 0.01 | 0.00 | 0.01 | 0.03 | 0.01 | 0.01 | 0.07 | 0.05 | 0.05 | 0.03 | 0.26 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.10 | 0.03 | 0.84 | 0.06 | 0.08 | 0.02 | 0.22 | 0.02 | 0.25 | 0.11 | 0.17 | 0.02 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.06 | 0.01 | 0.00 | 0.03 | 0.00 | 0.02 | 0.00 | 0.01 | 0.01 |
| HLA-B | ENSG00000234745 | 0.01 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.00 | 0.15 | 0.04 | 0.00 | 0.00 | 0.02 | 0.02 | 0.08 | 0.02 | 0.06 | 0.05 | 0.03 | 0.04 | 0.13 | 0.05 | 0.12 | 0.04 | 0.03 | 0.02 | 0.07 | 0.02 | 0.05 | 0.01 | 0.11 | 0.01 | 0.05 | 0.03 | 0.08 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.09 | 0.03 | 0.29 | 0.06 | 0.17 | 0.01 | 0.05 | 0.01 | 0.10 | 0.03 | 0.06 | 0.07 | 0.01 | 0.01 | 0.00 | 0.00 | 0.02 | 0.17 | 0.01 | 0.01 | 0.00 | 0.01 | 0.11 | 0.00 | 0.12 | 0.01 |
| LGALS3BP | ENSG00000108679 | 0.02 | 0.00 | 0.05 | 0.00 | 0.02 | 0.00 | 0.03 | 0.03 | 0.19 | 0.00 | 0.00 | 0.00 | 0.09 | 0.02 | 0.16 | 0.01 | 0.21 | 0.03 | 0.08 | 0.03 | 0.18 | 0.08 | 0.09 | 0.04 | 0.06 | 0.00 | 0.04 | 0.03 | 0.05 | 0.09 | 0.26 | 0.02 | 0.08 | 0.01 | 0.08 | 0.02 | 0.02 | 0.01 | 0.00 | 0.00 | 0.35 | 0.03 | 0.40 | 0.03 | 0.11 | 0.08 | 0.14 | 0.01 | 0.60 | 0.04 | 0.21 | 0.03 | 0.05 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.06 | 0.00 | 0.04 | 0.01 | 0.17 | 0.00 | 0.25 | 0.01 |
| HSP90AA1 | ENSG00000080824 | 0.00 | 0.02 | 0.01 | 0.01 | 0.00 | 0.04 | 0.03 | 0.03 | 0.08 | 0.09 | 0.00 | 0.00 | 0.00 | 0.08 | 0.06 | 0.06 | 0.17 | 0.03 | 0.05 | 0.06 | 0.08 | 0.06 | 0.04 | 0.08 | 0.00 | 0.03 | 0.02 | 0.04 | 0.01 | 0.03 | 0.00 | 0.10 | 0.00 | 0.31 | 0.05 | 0.00 | 0.01 | 0.04 | 0.00 | 0.00 | 0.08 | 0.07 | 0.25 | 0.16 | 0.06 | 0.10 | 0.09 | 0.02 | 0.06 | 0.02 | 0.11 | 0.05 | 0.04 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.08 | 0.02 | 0.06 | 0.03 | 0.01 | 0.01 | 0.06 |
| HDAC7 | ENSG00000061273 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.09 | 0.03 | 0.00 | 0.00 | 0.00 | 0.04 | 0.06 | 0.02 | 0.08 | 0.02 | 0.02 | 0.03 | 0.06 | 0.04 | 0.05 | 0.03 | 0.02 | 0.00 | 0.02 | 0.02 | 0.00 | 0.04 | 0.02 | 0.01 | 0.00 | 0.01 | 0.22 | 0.01 | 0.02 | 0.03 | 0.00 | 0.00 | 0.05 | 0.05 | 0.18 | 0.06 | 0.05 | 0.00 | 0.16 | 0.01 | 0.38 | 0.10 | 0.32 | 0.08 | 0.02 | 0.02 | 0.00 | 0.03 | 0.13 | 0.04 | 0.01 | 0.05 | 0.02 | 0.06 | 0.00 | 0.00 | 0.05 | 0.05 |
| SPOCK1 | ENSG00000152377 | 0.28 | 0.01 | 0.03 | 0.01 | 0.00 | 0.02 | 0.02 | 0.03 | 0.03 | 0.03 | 0.00 | 0.00 | 0.00 | 0.03 | 0.02 | 0.07 | 0.02 | 0.04 | 0.01 | 0.03 | 0.03 | 0.04 | 0.02 | 0.06 | 0.01 | 0.03 | 0.02 | 0.03 | 0.01 | 0.02 | 0.08 | 0.03 | 0.09 | 0.01 | 0.24 | 0.02 | 0.03 | 0.06 | 0.01 | 0.00 | 0.03 | 0.03 | 0.12 | 0.14 | 0.03 | 0.02 | 0.02 | 0.01 | 0.10 | 0.01 | 0.11 | 0.05 | 0.00 | 0.00 | 0.00 | 0.10 | 0.04 | 0.00 | 0.01 | 0.03 | 0.01 | 0.02 | 0.00 | 0.03 | 0.03 | 0.11 |
| CAMK2A | ENSG00000070808 | 0.31 | 0.00 | 0.02 | 0.01 | 0.03 | 0.00 | 0.02 | 0.01 | 0.03 | 0.05 | 0.00 | 0.00 | 0.02 | 0.05 | 0.04 | 0.04 | 0.01 | 0.03 | 0.02 | 0.04 | 0.04 | 0.02 | 0.03 | 0.04 | 0.02 | 0.01 | 0.04 | 0.01 | 0.02 | 0.02 | 0.10 | 0.02 | 0.09 | 0.01 | 0.26 | 0.04 | 0.00 | 0.03 | 0.01 | 0.00 | 0.04 | 0.02 | 0.19 | 0.09 | 0.02 | 0.01 | 0.05 | 0.02 | 0.11 | 0.02 | 0.08 | 0.05 | 0.00 | 0.00 | 0.00 | 0.10 | 0.04 | 0.00 | 0.00 | 0.06 | 0.02 | 0.03 | 0.00 | 0.03 | 0.04 | 0.14 |
| NCAN | ENSG00000130287 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.05 | 0.03 | 0.01 | 0.03 | 0.05 | 0.00 | 0.03 | 0.03 | 0.13 | 0.02 | 0.04 | 0.02 | 0.18 | 0.01 | 0.04 | 0.02 | 0.01 | 0.00 | 0.03 | 0.04 | 0.01 | 0.02 | 0.07 | 0.02 | 0.02 | 0.03 | 0.16 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.08 | 0.03 | 0.51 | 0.06 | 0.02 | 0.02 | 0.16 | 0.04 | 0.34 | 0.05 | 0.07 | 0.05 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.03 | 0.01 | 0.00 | 0.01 | 0.01 | 0.02 | 0.00 | 0.03 | 0.02 |
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