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 |
| TUFT1 | ENSG00000143367 | 0.03 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.07 | 0.00 | 0.58 | 0.01 | 0.02 | 0.00 | 0.11 | 0.02 | 0.41 | 0.00 | 0.30 | 0.00 | 0.06 | 0.01 | 0.33 | 0.00 | 0.23 | 0.00 | 0.02 | 0.00 | 0.17 | 0.00 | 0.07 | 0.00 | 0.38 | 0.00 | 0.43 | 0.01 | 0.20 | 0.00 | 0.10 | 0.00 | 0.00 | 0.00 | 0.36 | 0.01 | 0.68 | 0.02 | 0.22 | 0.00 | 0.30 | 0.00 | 0.71 | 0.00 | 0.49 | 0.02 | 0.12 | 0.01 | 0.00 | 0.00 | 0.24 | 0.04 | 0.01 | 0.00 | 0.05 | 0.00 | 0.00 | 0.00 | 0.22 | 0.00 |
| ALDH1A3 | ENSG00000184254 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.02 | 0.03 | 0.06 | 0.03 | 0.03 | 0.02 | 0.06 | 0.00 | 0.08 | 0.02 | 0.27 | 0.01 | 0.11 | 0.01 | 0.26 | 0.02 | 0.25 | 0.01 | 0.05 | 0.01 | 0.08 | 0.02 | 0.07 | 0.00 | 0.13 | 0.07 | 0.05 | 0.01 | 0.13 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.21 | 0.03 | 0.45 | 0.07 | 0.17 | 0.02 | 0.08 | 0.02 | 0.14 | 0.04 | 0.27 | 0.07 | 0.01 | 0.01 | 0.00 | 0.00 | 0.06 | 0.00 | 0.03 | 0.01 | 0.01 | 0.03 | 0.00 | 0.00 | 0.20 | 0.02 |
| CEACAM5 | ENSG00000105388 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.02 | 0.01 | 0.04 | 0.16 | 0.03 | 0.00 | 0.00 | 0.05 | 0.05 | 0.11 | 0.04 | 0.16 | 0.07 | 0.02 | 0.02 | 0.06 | 0.06 | 0.07 | 0.03 | 0.03 | 0.01 | 0.03 | 0.02 | 0.03 | 0.04 | 0.03 | 0.03 | 0.12 | 0.01 | 0.06 | 0.04 | 0.00 | 0.02 | 0.00 | 0.00 | 0.07 | 0.05 | 0.17 | 0.27 | 0.14 | 0.04 | 0.06 | 0.04 | 0.09 | 0.17 | 0.29 | 0.10 | 0.00 | 0.04 | 0.01 | 0.00 | 0.05 | 0.03 | 0.03 | 0.09 | 0.02 | 0.09 | 0.00 | 0.00 | 0.04 | 0.03 |
| ARID4A | ENSG00000032219 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.02 | 0.04 | 0.00 | 0.01 | 0.00 | 0.05 | 0.08 | 0.02 | 0.03 | 0.04 | 0.05 | 0.01 | 0.05 | 0.01 | 0.04 | 0.04 | 0.00 | 0.02 | 0.02 | 0.02 | 0.03 | 0.01 | 0.02 | 0.06 | 0.05 | 0.10 | 0.04 | 0.03 | 0.01 | 0.01 | 0.00 | 0.00 | 0.05 | 0.05 | 0.03 | 0.22 | 0.01 | 0.02 | 0.01 | 0.02 | 0.00 | 0.06 | 0.03 | 0.09 | 0.00 | 0.01 | 0.00 | 0.00 | 0.04 | 0.03 | 0.00 | 0.06 | 0.01 | 0.05 | 0.03 | 0.00 | 0.01 | 0.04 |
| HSD11B2 | ENSG00000176387 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.06 | 0.00 | 0.06 | 0.15 | 0.02 | 0.00 | 0.00 | 0.03 | 0.06 | 0.04 | 0.03 | 0.05 | 0.02 | 0.03 | 0.01 | 0.12 | 0.01 | 0.05 | 0.03 | 0.00 | 0.00 | 0.01 | 0.01 | 0.01 | 0.00 | 0.01 | 0.04 | 0.05 | 0.01 | 0.28 | 0.02 | 0.01 | 0.02 | 0.00 | 0.01 | 0.02 | 0.05 | 0.04 | 0.31 | 0.03 | 0.02 | 0.03 | 0.08 | 0.05 | 0.18 | 0.02 | 0.04 | 0.15 | 0.01 | 0.00 | 0.05 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.00 | 0.03 | 0.05 | 0.00 |
| NAPSA | ENSG00000131400 | 0.00 | 0.00 | 0.01 | 0.02 | 0.00 | 0.00 | 0.01 | 0.01 | 0.10 | 0.04 | 0.00 | 0.02 | 0.00 | 0.06 | 0.01 | 0.07 | 0.07 | 0.11 | 0.03 | 0.02 | 0.06 | 0.03 | 0.09 | 0.03 | 0.01 | 0.03 | 0.02 | 0.03 | 0.03 | 0.05 | 0.05 | 0.04 | 0.00 | 0.07 | 0.23 | 0.02 | 0.00 | 0.03 | 0.00 | 0.00 | 0.10 | 0.04 | 0.05 | 0.31 | 0.06 | 0.07 | 0.03 | 0.05 | 0.15 | 0.13 | 0.03 | 0.17 | 0.00 | 0.04 | 0.01 | 0.00 | 0.24 | 0.03 | 0.00 | 0.15 | 0.02 | 0.13 | 0.00 | 0.00 | 0.03 | 0.02 |
| MAP4K1 | ENSG00000104814 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.02 | 0.02 | 0.01 | 0.32 | 0.02 | 0.00 | 0.00 | 0.08 | 0.03 | 0.20 | 0.03 | 0.54 | 0.03 | 0.06 | 0.01 | 0.12 | 0.03 | 0.12 | 0.02 | 0.05 | 0.01 | 0.01 | 0.01 | 0.20 | 0.00 | 0.03 | 0.01 | 0.12 | 0.03 | 0.05 | 0.03 | 0.00 | 0.02 | 0.00 | 0.00 | 0.14 | 0.03 | 0.73 | 0.12 | 0.28 | 0.03 | 0.17 | 0.03 | 1.15 | 0.09 | 0.24 | 0.10 | 0.00 | 0.03 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.04 | 0.05 | 0.03 | 0.00 | 0.00 | 0.04 | 0.01 |
| PTPN14 | ENSG00000152104 | 0.01 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.06 | 0.07 | 0.06 | 0.01 | 0.00 | 0.07 | 0.04 | 0.08 | 0.02 | 0.10 | 0.03 | 0.05 | 0.02 | 0.16 | 0.05 | 0.06 | 0.01 | 0.05 | 0.00 | 0.07 | 0.03 | 0.00 | 0.02 | 0.15 | 0.03 | 0.16 | 0.02 | 0.03 | 0.04 | 0.02 | 0.01 | 0.00 | 0.00 | 0.20 | 0.02 | 0.20 | 0.18 | 0.06 | 0.01 | 0.07 | 0.03 | 0.23 | 0.04 | 0.02 | 0.21 | 0.03 | 0.03 | 0.01 | 0.00 | 0.15 | 0.04 | 0.00 | 0.02 | 0.02 | 0.06 | 0.09 | 0.00 | 0.11 | 0.03 |
| BCAT1 | ENSG00000060982 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.05 | 0.14 | 0.03 | 0.00 | 0.00 | 0.02 | 0.01 | 0.25 | 0.03 | 0.18 | 0.00 | 0.07 | 0.01 | 0.52 | 0.03 | 0.39 | 0.01 | 0.02 | 0.01 | 0.21 | 0.02 | 0.10 | 0.02 | 0.01 | 0.03 | 0.00 | 0.05 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.08 | 0.03 | 0.50 | 0.05 | 0.04 | 0.00 | 0.12 | 0.02 | 0.38 | 0.03 | 0.18 | 0.11 | 0.61 | 0.00 | 0.00 | 0.01 | 0.00 | 0.02 | 0.07 | 0.01 | 0.05 | 0.02 | 0.00 | 0.00 | 0.06 | 0.01 |
| ABCC3 | ENSG00000108846 | 0.01 | 0.00 | 0.05 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.15 | 0.01 | 0.01 | 0.00 | 0.09 | 0.00 | 0.09 | 0.01 | 0.13 | 0.01 | 0.02 | 0.01 | 0.19 | 0.00 | 0.12 | 0.01 | 0.03 | 0.00 | 0.07 | 0.04 | 0.06 | 0.02 | 0.08 | 0.01 | 0.02 | 0.01 | 0.11 | 0.03 | 0.02 | 0.03 | 0.00 | 0.00 | 0.49 | 0.02 | 0.17 | 0.03 | 0.07 | 0.00 | 0.11 | 0.02 | 0.48 | 0.00 | 0.12 | 0.02 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.03 | 0.00 | 0.03 | 0.03 | 0.14 | 0.02 |
| ADCYAP1R1 | ENSG00000078549 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.05 | 0.00 | 0.10 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.06 | 0.00 | 0.07 | 0.02 | 0.04 | 0.01 | 0.12 | 0.02 | 0.05 | 0.00 | 0.04 | 0.00 | 0.03 | 0.00 | 0.02 | 0.00 | 0.05 | 0.01 | 0.00 | 0.02 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.09 | 0.02 | 0.17 | 0.12 | 0.03 | 0.01 | 0.06 | 0.02 | 0.04 | 0.01 | 0.17 | 0.03 | 0.05 | 0.00 | 0.00 | 0.01 | 0.00 | 0.02 | 0.03 | 0.00 | 0.06 | 0.00 | 0.00 | 0.00 | 0.06 | 0.02 |
| MMP16 | ENSG00000156103 | 0.00 | 0.01 | 0.00 | 0.01 | 0.06 | 0.00 | 0.07 | 0.03 | 0.17 | 0.01 | 0.02 | 0.00 | 0.02 | 0.00 | 0.15 | 0.02 | 0.14 | 0.03 | 0.07 | 0.00 | 0.18 | 0.02 | 0.12 | 0.01 | 0.09 | 0.01 | 0.13 | 0.02 | 0.03 | 0.01 | 0.17 | 0.00 | 0.20 | 0.01 | 0.06 | 0.00 | 0.01 | 0.02 | 0.00 | 0.00 | 0.32 | 0.01 | 0.30 | 0.10 | 0.05 | 0.01 | 0.07 | 0.02 | 0.34 | 0.08 | 0.23 | 0.07 | 0.16 | 0.00 | 0.00 | 0.00 | 0.08 | 0.04 | 0.05 | 0.01 | 0.01 | 0.01 | 0.27 | 0.00 | 0.10 | 0.01 |
| GPC6 | ENSG00000183098 | 0.01 | 0.01 | 0.00 | 0.01 | 0.00 | 0.10 | 0.02 | 0.09 | 0.16 | 0.07 | 0.00 | 0.01 | 0.01 | 0.08 | 0.12 | 0.05 | 0.11 | 0.05 | 0.07 | 0.04 | 0.09 | 0.07 | 0.14 | 0.03 | 0.09 | 0.01 | 0.15 | 0.01 | 0.03 | 0.03 | 0.24 | 0.08 | 0.06 | 0.10 | 0.04 | 0.06 | 0.02 | 0.04 | 0.00 | 0.00 | 0.13 | 0.05 | 0.21 | 0.11 | 0.17 | 0.06 | 0.06 | 0.02 | 0.61 | 0.05 | 0.25 | 0.15 | 0.01 | 0.02 | 0.00 | 0.00 | 0.08 | 0.04 | 0.02 | 0.03 | 0.02 | 0.06 | 0.05 | 0.00 | 0.08 | 0.04 |
| LIPG | ENSG00000101670 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.02 | 0.07 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.08 | 0.03 | 0.04 | 0.04 | 0.07 | 0.05 | 0.18 | 0.04 | 0.14 | 0.02 | 0.05 | 0.00 | 0.08 | 0.00 | 0.08 | 0.03 | 0.07 | 0.00 | 0.05 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.05 | 0.07 | 0.23 | 0.01 | 0.04 | 0.02 | 0.04 | 0.01 | 0.01 | 0.07 | 0.05 | 0.01 | 0.00 | 0.00 | 0.01 | 0.05 | 0.00 | 0.01 | 0.02 | 0.00 | 0.02 | 0.00 | 0.01 | 0.02 | 0.01 |
| PASK | ENSG00000115687 | 0.01 | 0.08 | 0.04 | 0.05 | 0.00 | 0.10 | 0.01 | 0.04 | 0.00 | 0.33 | 0.00 | 0.02 | 0.00 | 0.07 | 0.05 | 0.05 | 0.03 | 0.19 | 0.02 | 0.18 | 0.03 | 0.17 | 0.03 | 0.10 | 0.02 | 0.03 | 0.04 | 0.04 | 0.04 | 0.04 | 0.04 | 0.09 | 0.10 | 0.01 | 0.05 | 0.10 | 0.00 | 0.01 | 0.00 | 0.01 | 0.03 | 0.11 | 0.21 | 0.29 | 0.02 | 0.38 | 0.03 | 0.07 | 0.17 | 0.09 | 0.06 | 0.49 | 0.03 | 0.07 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.15 | 0.00 | 0.04 | 0.01 | 0.08 | 0.01 | 0.15 |
| FLRT1 | ENSG00000126500 | 0.01 | 0.00 | 0.00 | 0.01 | 0.07 | 0.00 | 0.03 | 0.01 | 0.12 | 0.01 | 0.00 | 0.00 | 0.14 | 0.00 | 0.06 | 0.03 | 0.08 | 0.01 | 0.20 | 0.02 | 0.13 | 0.05 | 0.03 | 0.04 | 0.01 | 0.01 | 0.03 | 0.03 | 0.00 | 0.03 | 0.01 | 0.03 | 0.13 | 0.07 | 0.10 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.10 | 0.08 | 0.16 | 0.04 | 0.07 | 0.01 | 0.13 | 0.02 | 0.63 | 0.16 | 0.09 | 0.03 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.06 | 0.01 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.06 | 0.04 |
| BAMBI | ENSG00000095739 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.05 | 0.05 | 0.00 | 0.01 | 0.02 | 0.05 | 0.04 | 0.02 | 0.05 | 0.01 | 0.02 | 0.02 | 0.06 | 0.01 | 0.04 | 0.04 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.01 | 0.02 | 0.00 | 0.00 | 0.01 | 0.02 | 0.07 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.04 | 0.11 | 0.06 | 0.00 | 0.01 | 0.02 | 0.01 | 0.12 | 0.00 | 0.04 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 |
| LAMA3 | ENSG00000053747 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.09 | 0.02 | 0.00 | 0.00 | 0.03 | 0.01 | 0.15 | 0.01 | 0.22 | 0.02 | 0.16 | 0.03 | 0.50 | 0.04 | 0.27 | 0.03 | 0.01 | 0.02 | 0.04 | 0.02 | 0.25 | 0.03 | 0.01 | 0.00 | 0.04 | 0.03 | 0.08 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.02 | 0.32 | 0.04 | 0.02 | 0.03 | 0.12 | 0.00 | 0.04 | 0.07 | 0.11 | 0.03 | 0.00 | 0.03 | 0.00 | 0.01 | 0.03 | 0.00 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 |
| MATN3 | ENSG00000132031 | 0.00 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.02 | 0.02 | 0.11 | 0.00 | 0.00 | 0.00 | 0.03 | 0.05 | 0.05 | 0.02 | 0.11 | 0.03 | 0.04 | 0.02 | 0.07 | 0.05 | 0.05 | 0.04 | 0.01 | 0.01 | 0.01 | 0.02 | 0.01 | 0.04 | 0.13 | 0.00 | 0.00 | 0.05 | 0.01 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.05 | 0.21 | 0.15 | 0.10 | 0.01 | 0.12 | 0.03 | 0.21 | 0.03 | 0.03 | 0.11 | 0.18 | 0.01 | 0.00 | 0.00 | 0.02 | 0.03 | 0.02 | 0.01 | 0.04 | 0.02 | 0.05 | 0.00 | 0.01 | 0.04 |
| SCARB1 | ENSG00000073060 | 0.01 | 0.01 | 0.02 | 0.00 | 0.07 | 0.02 | 0.02 | 0.07 | 0.07 | 0.03 | 0.00 | 0.00 | 0.03 | 0.02 | 0.05 | 0.05 | 0.03 | 0.07 | 0.03 | 0.04 | 0.12 | 0.06 | 0.08 | 0.04 | 0.01 | 0.01 | 0.05 | 0.01 | 0.00 | 0.05 | 0.05 | 0.10 | 0.00 | 0.17 | 0.21 | 0.07 | 0.03 | 0.03 | 0.00 | 0.00 | 0.06 | 0.09 | 0.18 | 0.24 | 0.02 | 0.02 | 0.06 | 0.07 | 0.12 | 0.16 | 0.13 | 0.05 | 0.01 | 0.01 | 0.01 | 0.01 | 0.07 | 0.00 | 0.03 | 0.01 | 0.04 | 0.01 | 0.00 | 0.00 | 0.04 | 0.07 |
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