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 |
| ENOX1 | ENSG00000120658 | 0.00 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.38 | 0.04 | 0.23 | 0.00 | 0.02 | 0.00 | 0.16 | 0.02 | 0.08 | 0.01 | 0.11 | 0.01 | 0.15 | 0.08 | 0.09 | 0.13 | 0.04 | 0.13 | 0.03 | 0.14 | 0.03 | 0.01 | 0.02 | 0.00 | 0.25 | 0.00 | 0.14 | 0.00 | 0.07 | 0.01 | 0.00 | 0.00 | 0.01 | 0.03 | 0.13 | 0.06 | 0.23 | 0.01 | 0.23 | 0.01 | 0.05 | 0.12 | 0.23 | 0.07 | 0.33 | 0.00 | 0.02 | 0.00 | 0.00 | 0.09 | 0.06 | 0.01 | 0.06 | 0.00 | 0.12 | 0.00 | 0.00 | 0.02 | 0.04 |
| JARID2 | ENSG00000008083 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.01 | 0.38 | 0.03 | 0.00 | 0.01 | 0.01 | 0.03 | 0.09 | 0.01 | 0.09 | 0.07 | 0.05 | 0.05 | 0.09 | 0.17 | 0.06 | 0.08 | 0.02 | 0.04 | 0.01 | 0.03 | 0.03 | 0.06 | 0.15 | 0.01 | 0.06 | 0.03 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.17 | 0.04 | 0.50 | 0.05 | 0.09 | 0.05 | 0.05 | 0.02 | 0.21 | 0.02 | 0.07 | 0.13 | 0.04 | 0.16 | 0.00 | 0.00 | 0.05 | 0.01 | 0.02 | 0.02 | 0.02 | 0.01 | 0.25 | 0.00 | 0.22 | 0.01 |
| SCNN1A | ENSG00000111319 | 0.01 | 0.00 | 0.00 | 0.01 | 0.02 | 0.00 | 0.01 | 0.07 | 0.10 | 0.02 | 0.01 | 0.00 | 0.00 | 0.08 | 0.07 | 0.07 | 0.17 | 0.02 | 0.11 | 0.02 | 0.10 | 0.05 | 0.06 | 0.05 | 0.06 | 0.02 | 0.05 | 0.02 | 0.05 | 0.05 | 0.04 | 0.04 | 0.14 | 0.05 | 0.07 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.13 | 0.04 | 0.37 | 0.08 | 0.05 | 0.02 | 0.10 | 0.02 | 0.10 | 0.03 | 0.08 | 0.12 | 0.58 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.15 | 0.01 | 0.05 | 0.02 | 0.00 | 0.01 | 0.05 | 0.04 |
| CHRM1 | ENSG00000168539 | 0.00 | 0.00 | 0.00 | 0.01 | 0.09 | 0.00 | 0.02 | 0.01 | 0.13 | 0.01 | 0.00 | 0.00 | 0.12 | 0.02 | 0.05 | 0.02 | 0.06 | 0.01 | 0.13 | 0.03 | 0.13 | 0.02 | 0.04 | 0.02 | 0.01 | 0.02 | 0.02 | 0.03 | 0.00 | 0.03 | 0.02 | 0.02 | 0.05 | 0.07 | 0.08 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.09 | 0.07 | 0.17 | 0.03 | 0.06 | 0.01 | 0.09 | 0.02 | 0.29 | 0.12 | 0.06 | 0.02 | 0.00 | 0.07 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.04 | 0.05 |
| ATP9B | ENSG00000166377 | 0.00 | 0.02 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.11 | 0.02 | 0.13 | 0.00 | 0.00 | 0.01 | 0.04 | 0.03 | 0.11 | 0.04 | 0.14 | 0.01 | 0.20 | 0.07 | 0.20 | 0.05 | 0.17 | 0.01 | 0.10 | 0.01 | 0.15 | 0.00 | 0.05 | 0.04 | 0.07 | 0.00 | 0.18 | 0.04 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.09 | 0.10 | 0.44 | 0.04 | 0.06 | 0.04 | 0.10 | 0.12 | 0.12 | 0.17 | 0.15 | 0.00 | 0.10 | 0.00 | 0.02 | 0.08 | 0.05 | 0.03 | 0.06 | 0.03 | 0.05 | 0.00 | 0.04 | 0.02 | 0.03 |
| ABCB5 | ENSG00000004846 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.02 | 0.18 | 0.01 | 0.00 | 0.00 | 0.07 | 0.01 | 0.10 | 0.00 | 0.11 | 0.02 | 0.05 | 0.01 | 0.17 | 0.01 | 0.08 | 0.01 | 0.05 | 0.00 | 0.03 | 0.00 | 0.04 | 0.00 | 0.05 | 0.00 | 0.00 | 0.01 | 0.08 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.11 | 0.04 | 0.18 | 0.22 | 0.01 | 0.01 | 0.05 | 0.03 | 0.17 | 0.01 | 0.15 | 0.03 | 0.08 | 0.00 | 0.00 | 0.02 | 0.06 | 0.02 | 0.01 | 0.00 | 0.05 | 0.01 | 0.00 | 0.00 | 0.09 | 0.02 |
| SLCO5A1 | ENSG00000137571 | 0.00 | 0.01 | 0.00 | 0.01 | 0.08 | 0.00 | 0.06 | 0.01 | 0.11 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.16 | 0.02 | 0.10 | 0.02 | 0.06 | 0.01 | 0.09 | 0.01 | 0.09 | 0.02 | 0.06 | 0.00 | 0.13 | 0.03 | 0.02 | 0.01 | 0.10 | 0.00 | 0.06 | 0.02 | 0.04 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.20 | 0.02 | 0.40 | 0.07 | 0.05 | 0.01 | 0.11 | 0.01 | 0.39 | 0.02 | 0.14 | 0.07 | 0.22 | 0.00 | 0.01 | 0.00 | 0.04 | 0.03 | 0.01 | 0.01 | 0.00 | 0.02 | 0.22 | 0.00 | 0.07 | 0.01 |
| CACNG7 | ENSG00000105605 | 0.01 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.03 | 0.00 | 0.18 | 0.02 | 0.00 | 0.00 | 0.01 | 0.06 | 0.02 | 0.06 | 0.11 | 0.09 | 0.03 | 0.02 | 0.10 | 0.03 | 0.09 | 0.03 | 0.02 | 0.02 | 0.01 | 0.04 | 0.03 | 0.04 | 0.06 | 0.02 | 0.00 | 0.07 | 0.21 | 0.00 | 0.00 | 0.03 | 0.00 | 0.00 | 0.15 | 0.03 | 0.14 | 0.27 | 0.13 | 0.06 | 0.06 | 0.05 | 0.35 | 0.10 | 0.08 | 0.18 | 0.00 | 0.06 | 0.01 | 0.00 | 0.13 | 0.03 | 0.01 | 0.17 | 0.02 | 0.12 | 0.00 | 0.00 | 0.04 | 0.03 |
| FAAH | ENSG00000117480 | 0.00 | 0.02 | 0.01 | 0.03 | 0.00 | 0.05 | 0.00 | 0.04 | 0.10 | 0.03 | 0.00 | 0.00 | 0.09 | 0.03 | 0.08 | 0.03 | 0.08 | 0.02 | 0.05 | 0.01 | 0.03 | 0.02 | 0.03 | 0.03 | 0.02 | 0.02 | 0.02 | 0.02 | 0.01 | 0.01 | 0.01 | 0.08 | 0.00 | 0.23 | 0.02 | 0.03 | 0.01 | 0.12 | 0.00 | 0.00 | 0.05 | 0.05 | 0.41 | 0.06 | 0.09 | 0.01 | 0.11 | 0.01 | 0.38 | 0.03 | 0.10 | 0.04 | 0.04 | 0.03 | 0.03 | 0.00 | 0.00 | 0.03 | 0.00 | 0.01 | 0.02 | 0.00 | 0.00 | 0.07 | 0.06 | 0.02 |
| TMEFF2 | ENSG00000144339 | 0.03 | 0.02 | 0.08 | 0.01 | 0.00 | 0.01 | 0.02 | 0.02 | 0.05 | 0.07 | 0.00 | 0.00 | 0.00 | 0.02 | 0.04 | 0.01 | 0.15 | 0.04 | 0.14 | 0.05 | 0.13 | 0.02 | 0.07 | 0.04 | 0.02 | 0.01 | 0.02 | 0.03 | 0.07 | 0.01 | 0.06 | 0.02 | 0.00 | 0.01 | 0.02 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.08 | 0.02 | 0.37 | 0.05 | 0.13 | 0.02 | 0.06 | 0.01 | 0.01 | 0.03 | 0.05 | 0.08 | 0.07 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.01 | 0.00 | 0.01 | 0.02 | 0.00 | 0.02 | 0.02 |
| RPN1 | ENSG00000163902 | 0.01 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.08 | 0.02 | 0.04 | 0.01 | 0.00 | 0.01 | 0.00 | 0.01 | 0.03 | 0.01 | 0.11 | 0.01 | 0.06 | 0.00 | 0.13 | 0.04 | 0.06 | 0.02 | 0.01 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 | 0.00 | 0.05 | 0.03 | 0.02 | 0.00 | 0.05 | 0.00 | 0.00 | 0.04 | 0.04 | 0.27 | 0.04 | 0.10 | 0.00 | 0.07 | 0.00 | 0.21 | 0.05 | 0.06 | 0.07 | 0.01 | 0.01 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 | 0.06 | 0.00 | 0.00 | 0.02 | 0.05 |
| MTA2 | ENSG00000149480 | 0.01 | 0.00 | 0.00 | 0.01 | 0.09 | 0.00 | 0.01 | 0.01 | 0.14 | 0.01 | 0.00 | 0.00 | 0.12 | 0.00 | 0.05 | 0.02 | 0.05 | 0.02 | 0.14 | 0.03 | 0.12 | 0.02 | 0.04 | 0.03 | 0.01 | 0.02 | 0.02 | 0.03 | 0.00 | 0.03 | 0.03 | 0.02 | 0.12 | 0.07 | 0.10 | 0.00 | 0.02 | 0.02 | 0.00 | 0.00 | 0.10 | 0.07 | 0.16 | 0.04 | 0.06 | 0.01 | 0.10 | 0.02 | 0.38 | 0.12 | 0.06 | 0.03 | 0.00 | 0.06 | 0.00 | 0.00 | 0.00 | 0.02 | 0.02 | 0.01 | 0.00 | 0.04 | 0.00 | 0.00 | 0.04 | 0.05 |
| NLGN1 | ENSG00000169760 | 0.06 | 0.00 | 0.04 | 0.00 | 0.00 | 0.01 | 0.07 | 0.02 | 0.19 | 0.01 | 0.00 | 0.00 | 0.00 | 0.04 | 0.18 | 0.02 | 1.71 | 0.01 | 0.64 | 0.00 | 0.82 | 0.02 | 0.25 | 0.02 | 0.03 | 0.01 | 0.06 | 0.03 | 0.04 | 0.00 | 0.14 | 0.01 | 0.12 | 0.01 | 0.10 | 0.00 | 0.01 | 0.12 | 0.00 | 0.00 | 0.23 | 0.01 | 1.30 | 0.02 | 0.72 | 0.00 | 0.37 | 0.01 | 0.98 | 0.04 | 0.11 | 0.07 | 0.20 | 0.01 | 0.01 | 0.00 | 0.06 | 0.00 | 0.06 | 0.01 | 0.09 | 0.03 | 0.00 | 0.00 | 0.03 | 0.04 |
| SLC47A1 | ENSG00000142494 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.02 | 0.15 | 0.06 | 0.00 | 0.01 | 0.00 | 0.02 | 0.08 | 0.04 | 0.09 | 0.04 | 0.03 | 0.03 | 0.07 | 0.08 | 0.04 | 0.05 | 0.03 | 0.02 | 0.02 | 0.07 | 0.10 | 0.01 | 0.12 | 0.04 | 0.09 | 0.01 | 0.05 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.11 | 0.04 | 0.02 | 0.15 | 0.02 | 0.05 | 0.06 | 0.07 | 0.07 | 0.20 | 0.69 | 0.02 | 0.03 | 0.00 | 0.00 | 0.00 | 0.06 | 0.00 | 0.01 | 0.01 | 0.01 | 0.02 | 0.00 | 0.00 | 0.02 | 0.03 |
| HLA-C | ENSG00000204525 | 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 |
| SCNN1G | ENSG00000166828 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.11 | 0.03 | 0.00 | 0.00 | 0.00 | 0.05 | 0.04 | 0.01 | 0.03 | 0.01 | 0.02 | 0.02 | 0.02 | 0.01 | 0.02 | 0.01 | 0.02 | 0.01 | 0.02 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.04 | 0.01 | 0.08 | 0.06 | 0.01 | 0.01 | 0.03 | 0.01 | 0.21 | 0.03 | 0.01 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.09 | 0.00 | 0.00 | 0.02 | 0.00 | 0.06 | 0.00 | 0.00 | 0.01 | 0.03 |
| TMCO3 | ENSG00000150403 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.04 | 0.21 | 0.02 | 0.00 | 0.01 | 0.01 | 0.02 | 0.10 | 0.09 | 0.23 | 0.05 | 0.15 | 0.01 | 0.22 | 0.03 | 0.15 | 0.03 | 0.10 | 0.01 | 0.17 | 0.02 | 0.02 | 0.02 | 0.29 | 0.00 | 0.06 | 0.04 | 0.13 | 0.03 | 0.01 | 0.00 | 0.00 | 0.00 | 0.16 | 0.05 | 0.27 | 0.16 | 0.23 | 0.01 | 0.09 | 0.03 | 0.33 | 0.12 | 0.46 | 0.10 | 0.01 | 0.02 | 0.00 | 0.00 | 0.02 | 0.12 | 0.04 | 0.02 | 0.08 | 0.02 | 0.08 | 0.00 | 0.07 | 0.08 |
| GRIK2 | ENSG00000164418 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.33 | 0.04 | 0.12 | 0.00 | 0.01 | 0.00 | 0.14 | 0.01 | 0.06 | 0.03 | 0.04 | 0.02 | 0.05 | 0.04 | 0.10 | 0.05 | 0.09 | 0.01 | 0.05 | 0.02 | 0.03 | 0.03 | 0.04 | 0.03 | 0.08 | 0.00 | 0.11 | 0.07 | 0.06 | 0.00 | 0.04 | 0.00 | 0.00 | 0.10 | 0.09 | 0.17 | 0.18 | 0.01 | 0.03 | 0.05 | 0.03 | 0.10 | 0.07 | 0.13 | 0.11 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.30 | 0.01 | 0.01 | 0.00 | 0.06 | 0.05 | 0.03 | 0.02 | 0.09 |
| EPDR1 | ENSG00000086289 | 0.00 | 0.01 | 0.02 | 0.00 | 0.00 | 0.00 | 0.02 | 0.02 | 0.09 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.01 | 0.05 | 0.03 | 0.03 | 0.01 | 0.09 | 0.02 | 0.02 | 0.01 | 0.03 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.02 | 0.10 | 0.10 | 0.01 | 0.00 | 0.03 | 0.02 | 0.05 | 0.00 | 0.12 | 0.04 | 0.02 | 0.00 | 0.00 | 0.01 | 0.00 | 0.02 | 0.01 | 0.00 | 0.06 | 0.01 | 0.00 | 0.00 | 0.04 | 0.03 |
| SLC8A3 | ENSG00000100678 | 0.01 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.03 | 0.03 | 0.05 | 0.00 | 0.01 | 0.00 | 0.05 | 0.04 | 0.04 | 0.03 | 0.05 | 0.03 | 0.01 | 0.05 | 0.03 | 0.02 | 0.05 | 0.02 | 0.02 | 0.01 | 0.03 | 0.01 | 0.01 | 0.01 | 0.10 | 0.00 | 0.33 | 0.00 | 0.05 | 0.01 | 0.04 | 0.00 | 0.00 | 0.01 | 0.11 | 0.07 | 0.25 | 0.02 | 0.02 | 0.02 | 0.02 | 0.07 | 0.04 | 0.04 | 0.14 | 0.02 | 0.01 | 0.00 | 0.00 | 0.04 | 0.00 | 0.00 | 0.11 | 0.01 | 0.08 | 0.03 | 0.00 | 0.01 | 0.04 |
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