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 |
| GP1BB | ENSG00000203618 | 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 | 0.17 | 0.07 | 0.10 | 0.03 | 0.08 | 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 | 0.19 | 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 |
| OR2T5 | ENSG00000203661 | 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 |
| OR2L2 | ENSG00000203663 | 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 |
| CAPN8 | ENSG00000203697 | 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 |
| CR1 | ENSG00000203710 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.03 | 0.06 | 0.06 | 0.01 | 0.00 | 0.07 | 0.03 | 0.12 | 0.01 | 0.09 | 0.01 | 0.05 | 0.00 | 0.16 | 0.06 | 0.06 | 0.02 | 0.04 | 0.00 | 0.12 | 0.02 | 0.00 | 0.00 | 0.16 | 0.01 | 0.18 | 0.02 | 0.01 | 0.03 | 0.01 | 0.00 | 0.00 | 0.00 | 0.25 | 0.01 | 0.20 | 0.12 | 0.06 | 0.00 | 0.07 | 0.02 | 0.13 | 0.04 | 0.04 | 0.18 | 0.02 | 0.03 | 0.01 | 0.00 | 0.16 | 0.13 | 0.00 | 0.02 | 0.03 | 0.02 | 0.09 | 0.00 | 0.14 | 0.02 |
| RAET1G | ENSG00000203722 | 0.00 | 0.06 | 0.00 | 0.01 | 0.00 | 0.05 | 0.01 | 0.03 | 0.04 | 0.08 | 0.00 | 0.03 | 0.00 | 0.17 | 0.01 | 0.06 | 0.05 | 0.06 | 0.03 | 0.04 | 0.08 | 0.05 | 0.09 | 0.05 | 0.02 | 0.01 | 0.04 | 0.03 | 0.00 | 0.04 | 0.01 | 0.11 | 0.00 | 0.16 | 0.11 | 0.03 | 0.00 | 0.02 | 0.00 | 0.00 | 0.10 | 0.08 | 0.02 | 0.41 | 0.02 | 0.07 | 0.02 | 0.04 | 0.08 | 0.03 | 0.34 | 0.03 | 0.01 | 0.04 | 0.00 | 0.00 | 0.00 | 0.09 | 0.00 | 0.05 | 0.00 | 0.09 | 0.05 | 0.09 | 0.02 | 0.13 |
| GPR52 | ENSG00000203737 | 0.03 | 0.00 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.04 | 0.32 | 0.03 | 0.02 | 0.00 | 0.09 | 0.03 | 0.13 | 0.01 | 0.21 | 0.02 | 0.04 | 0.03 | 0.19 | 0.07 | 0.10 | 0.07 | 0.03 | 0.01 | 0.12 | 0.02 | 0.05 | 0.00 | 0.20 | 0.01 | 0.17 | 0.01 | 0.00 | 0.04 | 0.04 | 0.00 | 0.00 | 0.00 | 0.17 | 0.01 | 0.33 | 0.04 | 0.10 | 0.00 | 0.10 | 0.00 | 0.29 | 0.00 | 0.28 | 0.06 | 0.10 | 0.01 | 0.00 | 0.00 | 0.30 | 0.02 | 0.01 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.12 | 0.03 |
| FCGR3A | ENSG00000203747 | 0.03 | 0.00 | 0.01 | 0.01 | 0.00 | 0.03 | 0.02 | 0.04 | 0.83 | 0.01 | 0.02 | 0.00 | 0.10 | 0.01 | 0.27 | 0.00 | 0.27 | 0.00 | 0.05 | 0.00 | 0.29 | 0.01 | 0.13 | 0.00 | 0.03 | 0.00 | 0.14 | 0.00 | 0.06 | 0.00 | 0.30 | 0.00 | 0.30 | 0.01 | 0.16 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.30 | 0.01 | 0.37 | 0.02 | 0.17 | 0.00 | 0.13 | 0.00 | 0.28 | 0.00 | 0.36 | 0.03 | 0.10 | 0.00 | 0.00 | 0.00 | 0.25 | 0.00 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.18 | 0.01 |
| OR6K3 | ENSG00000203757 | 0.03 | 0.00 | 0.01 | 0.01 | 0.00 | 0.03 | 0.02 | 0.06 | 0.41 | 0.01 | 0.02 | 0.00 | 0.11 | 0.00 | 0.27 | 0.00 | 0.25 | 0.00 | 0.06 | 0.00 | 0.24 | 0.00 | 0.12 | 0.00 | 0.03 | 0.00 | 0.11 | 0.00 | 0.07 | 0.00 | 0.28 | 0.00 | 0.35 | 0.01 | 0.16 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.23 | 0.01 | 0.38 | 0.02 | 0.15 | 0.00 | 0.13 | 0.00 | 0.28 | 0.00 | 0.38 | 0.01 | 0.10 | 0.00 | 0.00 | 0.00 | 0.24 | 0.00 | 0.01 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.16 | 0.02 |
| DDO | ENSG00000203797 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.29 | 0.02 | 0.12 | 0.00 | 0.05 | 0.00 | 0.12 | 0.02 | 0.06 | 0.06 | 0.04 | 0.02 | 0.04 | 0.03 | 0.07 | 0.05 | 0.07 | 0.01 | 0.03 | 0.01 | 0.04 | 0.00 | 0.03 | 0.00 | 0.08 | 0.00 | 0.15 | 0.09 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.12 | 0.09 | 0.09 | 0.24 | 0.02 | 0.02 | 0.11 | 0.02 | 0.16 | 0.03 | 0.20 | 0.07 | 0.00 | 0.04 | 0.00 | 0.00 | 0.01 | 0.24 | 0.00 | 0.02 | 0.02 | 0.05 | 0.00 | 0.03 | 0.00 | 0.12 |
| PNLIPRP3 | ENSG00000203837 | 0.00 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.05 | 0.03 | 0.11 | 0.00 | 0.02 | 0.01 | 0.17 | 0.03 | 0.03 | 0.04 | 0.05 | 0.01 | 0.03 | 0.04 | 0.06 | 0.06 | 0.05 | 0.01 | 0.06 | 0.01 | 0.05 | 0.01 | 0.01 | 0.01 | 0.10 | 0.14 | 0.25 | 0.11 | 0.00 | 0.01 | 0.02 | 0.00 | 0.00 | 0.03 | 0.09 | 0.14 | 0.22 | 0.01 | 0.06 | 0.05 | 0.06 | 0.04 | 0.05 | 0.04 | 0.05 | 0.07 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.00 | 0.12 | 0.00 | 0.07 | 0.00 | 0.00 | 0.01 | 0.06 |
| HIST2H3A | ENSG00000203852 | 0.03 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.04 | 0.03 | 0.50 | 0.04 | 0.02 | 0.00 | 0.10 | 0.13 | 0.38 | 0.12 | 0.28 | 0.13 | 0.10 | 0.16 | 0.23 | 0.11 | 0.19 | 0.04 | 0.02 | 0.04 | 0.15 | 0.03 | 0.05 | 0.01 | 0.33 | 0.03 | 0.39 | 0.01 | 0.17 | 0.03 | 0.10 | 0.26 | 0.00 | 0.00 | 0.36 | 0.05 | 0.60 | 0.09 | 0.15 | 0.06 | 0.25 | 0.02 | 0.41 | 0.04 | 0.41 | 0.12 | 0.12 | 0.03 | 0.00 | 0.00 | 0.28 | 0.02 | 0.01 | 0.01 | 0.02 | 0.03 | 0.00 | 0.03 | 0.17 | 0.05 |
| HSD3B1 | ENSG00000203857 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.03 | 0.02 | 0.20 | 0.03 | 0.00 | 0.00 | 0.01 | 0.15 | 0.04 | 0.12 | 0.10 | 0.16 | 0.04 | 0.16 | 0.16 | 0.10 | 0.04 | 0.05 | 0.03 | 0.04 | 0.05 | 0.03 | 0.15 | 0.01 | 0.03 | 0.03 | 0.05 | 0.04 | 0.12 | 0.03 | 0.04 | 0.25 | 0.00 | 0.00 | 0.13 | 0.05 | 0.22 | 0.09 | 0.07 | 0.06 | 0.04 | 0.02 | 0.10 | 0.06 | 0.13 | 0.11 | 0.03 | 0.03 | 0.00 | 0.00 | 0.03 | 0.02 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.08 | 0.33 | 0.07 |
| DEFB110 | ENSG00000203970 | 0.00 | 0.01 | 0.01 | 0.03 | 0.00 | 0.00 | 0.01 | 0.01 | 0.09 | 0.04 | 0.00 | 0.00 | 0.00 | 0.02 | 0.07 | 0.02 | 0.21 | 0.04 | 0.05 | 0.03 | 0.27 | 0.02 | 0.15 | 0.02 | 0.02 | 0.01 | 0.12 | 0.01 | 0.01 | 0.01 | 0.08 | 0.00 | 0.00 | 0.03 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.11 | 0.03 | 0.20 | 0.06 | 0.08 | 0.04 | 0.04 | 0.01 | 0.20 | 0.03 | 0.07 | 0.03 | 0.02 | 0.01 | 0.00 | 0.00 | 0.09 | 0.02 | 0.01 | 0.00 | 0.00 | 0.04 | 0.01 | 0.00 | 0.03 | 0.02 |
| LCN8 | ENSG00000204001 | 0.00 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.03 | 0.01 | 0.07 | 0.02 | 0.00 | 0.00 | 0.00 | 0.02 | 0.06 | 0.03 | 0.08 | 0.02 | 0.08 | 0.05 | 0.20 | 0.01 | 0.15 | 0.02 | 0.03 | 0.01 | 0.10 | 0.04 | 0.01 | 0.00 | 0.07 | 0.04 | 0.06 | 0.01 | 0.16 | 0.02 | 0.01 | 0.01 | 0.00 | 0.00 | 0.06 | 0.06 | 0.20 | 0.22 | 0.06 | 0.02 | 0.10 | 0.04 | 0.18 | 0.09 | 0.06 | 0.17 | 0.03 | 0.03 | 0.01 | 0.00 | 0.05 | 0.00 | 0.02 | 0.01 | 0.04 | 0.01 | 0.00 | 0.00 | 0.04 | 0.03 |
| LIPN | ENSG00000204020 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.33 | 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 | 0.14 | 0.02 | 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 | 0.02 | 0.11 | 0.07 | 0.31 | 0.01 | 0.12 | 0.04 | 0.13 | 0.09 | 0.12 | 0.01 | 0.16 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.16 | 0.00 | 0.04 | 0.00 | 0.15 | 0.00 | 0.00 | 0.00 | 0.07 |
| LIPK | ENSG00000204021 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.33 | 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 | 0.14 | 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 | 0.02 | 0.11 | 0.07 | 0.31 | 0.01 | 0.12 | 0.04 | 0.13 | 0.06 | 0.12 | 0.01 | 0.16 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.16 | 0.00 | 0.04 | 0.00 | 0.15 | 0.00 | 0.00 | 0.00 | 0.07 |
| LRIT2 | ENSG00000204033 | 0.00 | 0.01 | 0.00 | 0.00 | 0.03 | 0.00 | 0.00 | 0.12 | 0.04 | 0.06 | 0.00 | 0.00 | 0.02 | 0.06 | 0.02 | 0.03 | 0.02 | 0.07 | 0.02 | 0.05 | 0.03 | 0.07 | 0.03 | 0.07 | 0.02 | 0.07 | 0.02 | 0.03 | 0.01 | 0.01 | 0.00 | 0.05 | 0.25 | 0.02 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.01 | 0.08 | 0.05 | 0.13 | 0.21 | 0.02 | 0.04 | 0.07 | 0.06 | 0.02 | 0.06 | 0.01 | 0.08 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.01 | 0.02 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.03 |
| NPY4R | ENSG00000204174 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.07 | 0.07 | 0.05 | 0.00 | 0.00 | 0.01 | 0.04 | 0.04 | 0.02 | 0.11 | 0.03 | 0.04 | 0.03 | 0.11 | 0.08 | 0.04 | 0.02 | 0.00 | 0.02 | 0.00 | 0.01 | 0.00 | 0.01 | 0.02 | 0.02 | 0.15 | 0.01 | 0.08 | 0.02 | 0.00 | 0.00 | 0.00 | 0.01 | 0.06 | 0.05 | 0.09 | 0.14 | 0.01 | 0.02 | 0.02 | 0.03 | 0.05 | 0.06 | 0.05 | 0.10 | 0.01 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 | 0.01 | 0.02 | 0.00 | 0.00 | 0.02 | 0.02 |
| SYT15 | ENSG00000204176 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.07 | 0.07 | 0.05 | 0.00 | 0.00 | 0.01 | 0.04 | 0.04 | 0.02 | 0.11 | 0.03 | 0.04 | 0.03 | 0.11 | 0.08 | 0.04 | 0.02 | 0.00 | 0.02 | 0.00 | 0.01 | 0.00 | 0.01 | 0.02 | 0.02 | 0.15 | 0.01 | 0.08 | 0.02 | 0.00 | 0.00 | 0.00 | 0.01 | 0.06 | 0.05 | 0.09 | 0.14 | 0.01 | 0.02 | 0.02 | 0.03 | 0.05 | 0.06 | 0.05 | 0.10 | 0.01 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 | 0.01 | 0.02 | 0.00 | 0.00 | 0.02 | 0.02 |
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