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 |
| OR4N4 | ENSG00000183706 | 0.01 | 0.01 | 0.01 | 0.03 | 0.14 | 0.00 | 0.04 | 0.03 | 0.12 | 0.09 | 0.00 | 0.01 | 0.01 | 0.17 | 0.04 | 0.11 | 0.11 | 0.08 | 0.06 | 0.05 | 0.13 | 0.10 | 0.01 | 0.09 | 0.01 | 0.08 | 0.05 | 0.04 | 0.00 | 0.04 | 0.02 | 0.04 | 0.00 | 0.04 | 0.09 | 0.08 | 0.00 | 0.01 | 0.00 | 0.00 | 0.07 | 0.13 | 0.10 | 0.25 | 0.06 | 0.03 | 0.02 | 0.06 | 0.17 | 0.42 | 0.14 | 0.11 | 0.05 | 0.03 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.05 | 0.00 | 0.00 | 0.05 | 0.09 |
| IFNL2 | ENSG00000183709 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.02 | 0.01 | 0.02 | 0.29 | 0.02 | 0.00 | 0.00 | 0.08 | 0.01 | 0.17 | 0.03 | 0.55 | 0.03 | 0.09 | 0.01 | 0.10 | 0.03 | 0.13 | 0.02 | 0.07 | 0.01 | 0.01 | 0.01 | 0.28 | 0.00 | 0.06 | 0.02 | 0.12 | 0.01 | 0.11 | 0.03 | 0.00 | 0.02 | 0.00 | 0.00 | 0.15 | 0.03 | 0.77 | 0.13 | 0.26 | 0.03 | 0.21 | 0.03 | 1.17 | 0.09 | 0.26 | 0.09 | 0.00 | 0.03 | 0.01 | 0.00 | 0.05 | 0.00 | 0.04 | 0.05 | 0.06 | 0.04 | 0.00 | 0.00 | 0.04 | 0.01 |
| NPBWR1 | ENSG00000183729 | 0.00 | 0.00 | 0.00 | 0.00 | 0.08 | 0.00 | 0.05 | 0.02 | 0.12 | 0.02 | 0.00 | 0.00 | 0.00 | 0.07 | 0.09 | 0.02 | 0.14 | 0.03 | 0.06 | 0.01 | 0.08 | 0.03 | 0.07 | 0.02 | 0.06 | 0.02 | 0.11 | 0.01 | 0.01 | 0.01 | 0.03 | 0.02 | 0.00 | 0.02 | 0.03 | 0.00 | 0.01 | 0.02 | 0.00 | 0.00 | 0.14 | 0.03 | 0.39 | 0.02 | 0.02 | 0.01 | 0.12 | 0.01 | 0.73 | 0.09 | 0.11 | 0.04 | 0.15 | 0.00 | 0.01 | 0.00 | 0.00 | 0.06 | 0.00 | 0.00 | 0.01 | 0.01 | 0.20 | 0.00 | 0.07 | 0.02 |
| CBX6 | ENSG00000183741 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.08 | 0.06 | 0.00 | 0.05 | 0.00 | 0.02 | 0.06 | 0.03 | 0.09 | 0.02 | 0.02 | 0.01 | 0.03 | 0.00 | 0.01 | 0.02 | 0.01 | 0.02 | 0.02 | 0.02 | 0.01 | 0.02 | 0.04 | 0.01 | 0.00 | 0.01 | 0.02 | 0.01 | 0.00 | 0.05 | 0.00 | 0.00 | 0.03 | 0.02 | 0.11 | 0.12 | 0.03 | 0.01 | 0.06 | 0.02 | 0.39 | 0.10 | 0.07 | 0.03 | 0.01 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.02 | 0.01 | 0.04 | 0.02 | 0.00 | 0.20 | 0.01 |
| AIFM3 | ENSG00000183773 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.05 | 0.19 | 0.06 | 0.03 | 0.01 | 0.04 | 0.05 | 0.14 | 0.03 | 0.29 | 0.07 | 0.08 | 0.03 | 0.06 | 0.07 | 0.08 | 0.04 | 0.02 | 0.01 | 0.05 | 0.03 | 0.00 | 0.02 | 0.03 | 0.03 | 0.03 | 0.10 | 0.06 | 0.14 | 0.00 | 0.01 | 0.00 | 0.00 | 0.07 | 0.05 | 0.25 | 0.07 | 0.04 | 0.01 | 0.08 | 0.06 | 0.43 | 0.04 | 0.21 | 0.07 | 0.29 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.03 | 0.03 | 0.00 | 0.00 | 0.14 | 0.03 |
| TUBA8 | ENSG00000183785 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.05 | 0.17 | 0.06 | 0.03 | 0.01 | 0.08 | 0.05 | 0.07 | 0.03 | 0.18 | 0.07 | 0.10 | 0.03 | 0.09 | 0.07 | 0.05 | 0.04 | 0.02 | 0.01 | 0.06 | 0.03 | 0.00 | 0.02 | 0.02 | 0.03 | 0.08 | 0.10 | 0.10 | 0.14 | 0.01 | 0.01 | 0.02 | 0.00 | 0.06 | 0.05 | 0.20 | 0.07 | 0.05 | 0.01 | 0.06 | 0.06 | 0.42 | 0.04 | 0.14 | 0.07 | 0.13 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.01 | 0.03 | 0.00 | 0.00 | 0.13 | 0.03 |
| CCR4 | ENSG00000183813 | 0.00 | 0.18 | 0.00 | 0.01 | 0.08 | 0.00 | 0.01 | 0.01 | 0.16 | 0.03 | 0.00 | 0.03 | 0.02 | 0.19 | 0.01 | 0.03 | 0.02 | 0.04 | 0.00 | 0.04 | 0.08 | 0.04 | 0.05 | 0.06 | 0.00 | 0.03 | 0.03 | 0.02 | 0.01 | 0.02 | 0.06 | 0.01 | 0.00 | 0.16 | 0.05 | 0.01 | 0.01 | 0.03 | 0.00 | 0.00 | 0.06 | 0.06 | 0.12 | 0.17 | 0.04 | 0.01 | 0.05 | 0.03 | 0.13 | 0.13 | 0.12 | 0.05 | 0.05 | 0.04 | 0.00 | 0.01 | 0.04 | 0.09 | 0.02 | 0.01 | 0.00 | 0.03 | 0.00 | 0.03 | 0.02 | 0.04 |
| CNGA2 | ENSG00000183862 | 0.03 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.02 | 0.01 | 0.10 | 0.04 | 0.06 | 0.00 | 0.06 | 0.01 | 0.20 | 0.01 | 0.17 | 0.02 | 0.11 | 0.00 | 0.17 | 0.01 | 0.15 | 0.02 | 0.04 | 0.01 | 0.10 | 0.02 | 0.06 | 0.00 | 0.09 | 0.02 | 0.10 | 0.01 | 0.16 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.09 | 0.03 | 0.40 | 0.10 | 0.20 | 0.02 | 0.09 | 0.02 | 0.16 | 0.07 | 0.16 | 0.09 | 0.00 | 0.02 | 0.00 | 0.00 | 0.15 | 0.04 | 0.02 | 0.03 | 0.02 | 0.02 | 0.05 | 0.00 | 0.07 | 0.01 |
| ARSI | ENSG00000183876 | 0.30 | 0.00 | 0.02 | 0.01 | 0.03 | 0.00 | 0.02 | 0.01 | 0.02 | 0.05 | 0.00 | 0.00 | 0.02 | 0.05 | 0.04 | 0.04 | 0.01 | 0.03 | 0.02 | 0.04 | 0.04 | 0.01 | 0.04 | 0.03 | 0.01 | 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 | 0.18 | 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 |
| UTY | ENSG00000183878 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |
| LRRC55 | ENSG00000183908 | 0.00 | 0.00 | 0.00 | 0.01 | 0.09 | 0.00 | 0.00 | 0.01 | 0.13 | 0.02 | 0.00 | 0.00 | 0.06 | 0.03 | 0.05 | 0.03 | 0.08 | 0.02 | 0.12 | 0.01 | 0.12 | 0.04 | 0.00 | 0.04 | 0.01 | 0.01 | 0.01 | 0.03 | 0.00 | 0.02 | 0.02 | 0.02 | 0.00 | 0.12 | 0.04 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.12 | 0.06 | 0.11 | 0.04 | 0.06 | 0.02 | 0.03 | 0.02 | 0.31 | 0.11 | 0.07 | 0.05 | 0.01 | 0.03 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.01 | 0.01 | 0.02 | 0.00 | 0.00 | 0.05 | 0.02 |
| SDR42E2 | ENSG00000183921 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.13 | 0.04 | 0.00 | 0.00 | 0.00 | 0.04 | 0.03 | 0.02 | 0.04 | 0.02 | 0.02 | 0.02 | 0.03 | 0.02 | 0.02 | 0.01 | 0.02 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.10 | 0.06 | 0.01 | 0.01 | 0.03 | 0.01 | 0.15 | 0.00 | 0.02 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.09 | 0.00 | 0.00 | 0.02 | 0.00 | 0.07 | 0.00 | 0.00 | 0.01 | 0.03 |
| KCNH8 | ENSG00000183960 | 0.01 | 0.18 | 0.00 | 0.01 | 0.07 | 0.00 | 0.01 | 0.02 | 0.24 | 0.03 | 0.00 | 0.03 | 0.02 | 0.04 | 0.01 | 0.05 | 0.01 | 0.04 | 0.01 | 0.03 | 0.02 | 0.03 | 0.05 | 0.05 | 0.01 | 0.04 | 0.03 | 0.06 | 0.01 | 0.02 | 0.06 | 0.01 | 0.03 | 0.18 | 0.06 | 0.01 | 0.00 | 0.04 | 0.00 | 0.00 | 0.09 | 0.03 | 0.10 | 0.21 | 0.01 | 0.02 | 0.04 | 0.04 | 0.05 | 0.09 | 0.17 | 0.02 | 0.05 | 0.05 | 0.00 | 0.00 | 0.00 | 0.06 | 0.03 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.02 | 0.05 |
| NPW | ENSG00000183971 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.02 | 0.15 | 0.00 | 0.00 | 0.04 | 0.04 | 0.04 | 0.04 | 0.03 | 0.08 | 0.04 | 0.03 | 0.04 | 0.09 | 0.03 | 0.07 | 0.03 | 0.03 | 0.04 | 0.03 | 0.02 | 0.02 | 0.06 | 0.03 | 0.00 | 0.05 | 0.13 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.10 | 0.02 | 0.11 | 0.18 | 0.10 | 0.04 | 0.07 | 0.03 | 0.28 | 0.08 | 0.10 | 0.04 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.02 | 0.02 | 0.00 | 0.00 | 0.04 | 0.02 |
| NPB | ENSG00000183979 | 0.02 | 0.00 | 0.05 | 0.00 | 0.02 | 0.00 | 0.03 | 0.02 | 0.22 | 0.00 | 0.00 | 0.00 | 0.12 | 0.02 | 0.17 | 0.02 | 0.19 | 0.07 | 0.07 | 0.06 | 0.13 | 0.10 | 0.11 | 0.04 | 0.05 | 0.00 | 0.04 | 0.02 | 0.02 | 0.09 | 0.31 | 0.01 | 0.15 | 0.01 | 0.27 | 0.00 | 0.03 | 0.01 | 0.00 | 0.00 | 0.33 | 0.05 | 0.41 | 0.06 | 0.10 | 0.09 | 0.19 | 0.01 | 0.78 | 0.08 | 0.18 | 0.11 | 0.06 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.07 | 0.01 | 0.04 | 0.02 | 0.14 | 0.00 | 0.24 | 0.03 |
| PTP4A2 | ENSG00000184007 | 0.00 | 0.04 | 0.00 | 0.06 | 0.00 | 0.00 | 0.03 | 0.02 | 0.03 | 0.07 | 0.00 | 0.01 | 0.11 | 0.07 | 0.05 | 0.04 | 0.05 | 0.06 | 0.04 | 0.05 | 0.08 | 0.10 | 0.04 | 0.07 | 0.02 | 0.10 | 0.01 | 0.13 | 0.01 | 0.03 | 0.00 | 0.19 | 0.00 | 0.70 | 0.00 | 0.03 | 0.03 | 0.08 | 0.00 | 0.00 | 0.07 | 0.09 | 0.29 | 0.25 | 0.06 | 0.02 | 0.08 | 0.08 | 0.21 | 0.06 | 0.12 | 0.06 | 0.03 | 0.03 | 0.02 | 0.00 | 0.00 | 0.07 | 0.00 | 0.01 | 0.03 | 0.05 | 0.00 | 0.07 | 0.06 | 0.05 |
| OR2T10 | ENSG00000184022 | 0.01 | 0.02 | 0.01 | 0.01 | 0.00 | 0.01 | 0.02 | 0.04 | 0.14 | 0.04 | 0.02 | 0.02 | 0.08 | 0.05 | 0.13 | 0.01 | 0.17 | 0.03 | 0.10 | 0.02 | 0.27 | 0.04 | 0.13 | 0.01 | 0.04 | 0.02 | 0.08 | 0.01 | 0.02 | 0.01 | 0.20 | 0.02 | 0.23 | 0.02 | 0.10 | 0.07 | 0.00 | 0.04 | 0.00 | 0.00 | 0.29 | 0.02 | 0.48 | 0.12 | 0.13 | 0.01 | 0.12 | 0.02 | 0.32 | 0.00 | 0.09 | 0.24 | 0.06 | 0.02 | 0.01 | 0.00 | 0.03 | 0.18 | 0.02 | 0.04 | 0.02 | 0.04 | 0.15 | 0.03 | 0.24 | 0.02 |
| OR7E87P | ENSG00000184055 | 0.01 | 0.01 | 0.01 | 0.01 | 0.09 | 0.00 | 0.04 | 0.00 | 0.26 | 0.03 | 0.00 | 0.00 | 0.08 | 0.00 | 0.14 | 0.01 | 0.40 | 0.02 | 0.93 | 0.03 | 1.30 | 0.02 | 0.14 | 0.02 | 0.01 | 0.01 | 0.02 | 0.02 | 0.03 | 0.02 | 0.10 | 0.02 | 0.00 | 0.06 | 0.01 | 0.01 | 0.02 | 0.00 | 0.00 | 0.00 | 0.45 | 0.05 | 0.44 | 0.04 | 0.17 | 0.01 | 0.07 | 0.02 | 0.18 | 0.11 | 0.10 | 0.07 | 0.00 | 0.06 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.24 | 0.01 |
| OR4F6 | ENSG00000184140 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.02 | 0.03 | 0.07 | 0.03 | 0.03 | 0.00 | 0.06 | 0.00 | 0.07 | 0.02 | 0.27 | 0.02 | 0.11 | 0.01 | 0.21 | 0.03 | 0.22 | 0.01 | 0.05 | 0.01 | 0.08 | 0.02 | 0.07 | 0.00 | 0.14 | 0.07 | 0.05 | 0.01 | 0.16 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.21 | 0.04 | 0.44 | 0.08 | 0.17 | 0.02 | 0.07 | 0.02 | 0.14 | 0.04 | 0.29 | 0.09 | 0.01 | 0.01 | 0.00 | 0.00 | 0.06 | 0.00 | 0.03 | 0.01 | 0.02 | 0.02 | 0.00 | 0.00 | 0.20 | 0.03 |
| LRTOMT | ENSG00000184154 | 0.00 | 0.01 | 0.01 | 0.01 | 0.10 | 0.02 | 0.04 | 0.00 | 0.23 | 0.03 | 0.00 | 0.00 | 0.08 | 0.02 | 0.12 | 0.01 | 0.21 | 0.03 | 0.49 | 0.03 | 0.92 | 0.03 | 0.14 | 0.03 | 0.01 | 0.01 | 0.02 | 0.02 | 0.02 | 0.02 | 0.07 | 0.03 | 0.00 | 0.02 | 0.05 | 0.01 | 0.03 | 0.00 | 0.00 | 0.00 | 0.27 | 0.06 | 0.44 | 0.04 | 0.12 | 0.01 | 0.06 | 0.01 | 0.16 | 0.10 | 0.12 | 0.06 | 0.00 | 0.06 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.00 | 0.01 | 0.02 | 0.00 | 0.00 | 0.27 | 0.01 |
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