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 |
| TUBG1 | ENSG00000131462 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.09 | 0.04 | 0.02 | 0.01 | 0.00 | 0.01 | 0.02 | 0.07 | 0.01 | 0.02 | 0.05 | 0.03 | 0.01 | 0.13 | 0.02 | 0.12 | 0.04 | 0.04 | 0.01 | 0.03 | 0.02 | 0.03 | 0.03 | 0.05 | 0.03 | 0.02 | 0.01 | 0.01 | 0.14 | 0.01 | 0.12 | 0.00 | 0.00 | 0.04 | 0.10 | 0.01 | 0.15 | 0.02 | 0.03 | 0.02 | 0.08 | 0.01 | 0.20 | 0.05 | 0.09 | 0.01 | 0.01 | 0.00 | 0.02 | 0.02 | 0.00 | 0.00 | 0.01 | 0.01 | 0.02 | 0.00 | 0.05 | 0.01 | 0.03 |
| AOC3 | ENSG00000131471 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.08 | 0.05 | 0.02 | 0.01 | 0.01 | 0.03 | 0.02 | 0.06 | 0.01 | 0.03 | 0.05 | 0.02 | 0.01 | 0.12 | 0.01 | 0.11 | 0.03 | 0.04 | 0.01 | 0.03 | 0.03 | 0.03 | 0.03 | 0.04 | 0.04 | 0.02 | 0.01 | 0.01 | 0.14 | 0.01 | 0.11 | 0.00 | 0.00 | 0.05 | 0.10 | 0.01 | 0.15 | 0.02 | 0.03 | 0.03 | 0.08 | 0.00 | 0.19 | 0.05 | 0.10 | 0.02 | 0.01 | 0.00 | 0.02 | 0.02 | 0.00 | 0.00 | 0.01 | 0.01 | 0.02 | 0.00 | 0.05 | 0.01 | 0.03 |
| RAMP2 | ENSG00000131477 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.09 | 0.04 | 0.02 | 0.01 | 0.01 | 0.02 | 0.02 | 0.06 | 0.01 | 0.03 | 0.05 | 0.02 | 0.01 | 0.13 | 0.02 | 0.11 | 0.03 | 0.04 | 0.01 | 0.03 | 0.03 | 0.03 | 0.03 | 0.04 | 0.03 | 0.02 | 0.01 | 0.01 | 0.14 | 0.01 | 0.12 | 0.00 | 0.00 | 0.05 | 0.10 | 0.01 | 0.15 | 0.02 | 0.03 | 0.03 | 0.08 | 0.00 | 0.19 | 0.04 | 0.10 | 0.01 | 0.01 | 0.00 | 0.02 | 0.02 | 0.00 | 0.00 | 0.01 | 0.01 | 0.02 | 0.00 | 0.05 | 0.01 | 0.03 |
| AOC2 | ENSG00000131480 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.08 | 0.06 | 0.02 | 0.01 | 0.01 | 0.03 | 0.02 | 0.06 | 0.01 | 0.03 | 0.05 | 0.02 | 0.01 | 0.12 | 0.01 | 0.11 | 0.03 | 0.04 | 0.01 | 0.03 | 0.03 | 0.03 | 0.03 | 0.04 | 0.04 | 0.02 | 0.01 | 0.01 | 0.14 | 0.01 | 0.11 | 0.00 | 0.00 | 0.05 | 0.10 | 0.01 | 0.15 | 0.02 | 0.03 | 0.03 | 0.08 | 0.00 | 0.19 | 0.04 | 0.10 | 0.02 | 0.01 | 0.00 | 0.02 | 0.02 | 0.00 | 0.00 | 0.01 | 0.01 | 0.02 | 0.00 | 0.05 | 0.02 | 0.03 |
| G6PC | ENSG00000131482 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.08 | 0.05 | 0.02 | 0.01 | 0.01 | 0.03 | 0.02 | 0.06 | 0.01 | 0.03 | 0.05 | 0.02 | 0.01 | 0.12 | 0.01 | 0.10 | 0.03 | 0.04 | 0.01 | 0.03 | 0.03 | 0.03 | 0.03 | 0.03 | 0.04 | 0.02 | 0.01 | 0.01 | 0.14 | 0.01 | 0.11 | 0.00 | 0.00 | 0.04 | 0.10 | 0.02 | 0.16 | 0.02 | 0.03 | 0.02 | 0.08 | 0.00 | 0.19 | 0.05 | 0.10 | 0.02 | 0.01 | 0.00 | 0.02 | 0.02 | 0.00 | 0.00 | 0.01 | 0.01 | 0.02 | 0.00 | 0.05 | 0.01 | 0.03 |
| NDFIP1 | ENSG00000131507 | 0.30 | 0.00 | 0.03 | 0.01 | 0.00 | 0.00 | 0.03 | 0.02 | 0.02 | 0.04 | 0.00 | 0.00 | 0.00 | 0.04 | 0.02 | 0.04 | 0.01 | 0.03 | 0.01 | 0.04 | 0.02 | 0.03 | 0.03 | 0.05 | 0.01 | 0.01 | 0.02 | 0.01 | 0.02 | 0.03 | 0.07 | 0.03 | 0.09 | 0.01 | 0.22 | 0.02 | 0.00 | 0.05 | 0.01 | 0.00 | 0.03 | 0.02 | 0.14 | 0.11 | 0.02 | 0.01 | 0.02 | 0.02 | 0.09 | 0.01 | 0.06 | 0.05 | 0.00 | 0.00 | 0.00 | 0.10 | 0.04 | 0.00 | 0.00 | 0.05 | 0.02 | 0.02 | 0.00 | 0.03 | 0.03 | 0.15 |
| TNS4 | ENSG00000131746 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.12 | 0.02 | 0.00 | 0.01 | 0.01 | 0.04 | 0.09 | 0.01 | 0.11 | 0.04 | 0.08 | 0.01 | 0.65 | 0.03 | 0.60 | 0.01 | 0.14 | 0.00 | 0.15 | 0.00 | 0.04 | 0.03 | 0.02 | 0.03 | 0.02 | 0.01 | 0.01 | 0.17 | 0.00 | 0.11 | 0.00 | 0.00 | 0.28 | 0.09 | 0.04 | 0.16 | 0.05 | 0.04 | 0.09 | 0.07 | 0.28 | 0.09 | 0.08 | 0.13 | 0.01 | 0.01 | 0.00 | 0.02 | 0.04 | 0.00 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.05 | 0.02 | 0.03 |
| PRKAB2 | ENSG00000131791 | 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 |
| FSHB | ENSG00000131808 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.03 | 0.06 | 0.00 | 0.00 | 0.00 | 0.04 | 0.04 | 0.02 | 0.07 | 0.02 | 0.02 | 0.03 | 0.16 | 0.03 | 0.04 | 0.02 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.03 | 0.01 | 0.00 | 0.00 | 0.01 | 0.02 | 0.01 | 0.02 | 0.04 | 0.00 | 0.00 | 0.09 | 0.02 | 0.20 | 0.06 | 0.00 | 0.03 | 0.06 | 0.02 | 0.07 | 0.05 | 0.12 | 0.12 | 0.01 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.03 | 0.02 | 0.00 | 0.00 | 0.00 | 0.01 |
| MCCC2 | ENSG00000131844 | 0.00 | 0.01 | 0.00 | 0.01 | 0.06 | 0.01 | 0.00 | 0.21 | 0.01 | 0.13 | 0.00 | 0.01 | 0.00 | 0.05 | 0.01 | 0.07 | 0.01 | 0.09 | 0.01 | 0.07 | 0.01 | 0.16 | 0.02 | 0.13 | 0.00 | 0.06 | 0.00 | 0.07 | 0.00 | 0.07 | 0.00 | 0.04 | 0.00 | 0.13 | 0.05 | 0.00 | 0.00 | 0.04 | 0.00 | 0.00 | 0.01 | 0.10 | 0.02 | 0.72 | 0.00 | 0.06 | 0.02 | 0.11 | 0.04 | 0.35 | 0.02 | 0.05 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.04 | 0.04 |
| VIMP | ENSG00000131871 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.02 | 0.03 | 0.06 | 0.03 | 0.03 | 0.00 | 0.06 | 0.00 | 0.07 | 0.02 | 0.28 | 0.02 | 0.11 | 0.01 | 0.21 | 0.03 | 0.23 | 0.01 | 0.05 | 0.01 | 0.08 | 0.02 | 0.07 | 0.00 | 0.14 | 0.07 | 0.05 | 0.01 | 0.19 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.20 | 0.04 | 0.45 | 0.08 | 0.17 | 0.02 | 0.08 | 0.02 | 0.14 | 0.04 | 0.28 | 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 | 0.02 |
| CHSY1 | ENSG00000131873 | 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 | 0.04 | 0.28 | 0.02 | 0.11 | 0.01 | 0.25 | 0.03 | 0.23 | 0.01 | 0.05 | 0.01 | 0.08 | 0.02 | 0.07 | 0.00 | 0.15 | 0.07 | 0.05 | 0.01 | 0.19 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.20 | 0.04 | 0.45 | 0.08 | 0.17 | 0.02 | 0.08 | 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 | 0.21 | 0.02 |
| NR0B2 | ENSG00000131910 | 0.00 | 0.06 | 0.00 | 0.08 | 0.00 | 0.00 | 0.01 | 0.02 | 0.06 | 0.10 | 0.00 | 0.01 | 0.05 | 0.19 | 0.04 | 0.07 | 0.02 | 0.11 | 0.03 | 0.08 | 0.03 | 0.17 | 0.01 | 0.15 | 0.00 | 0.18 | 0.00 | 0.22 | 0.00 | 0.11 | 0.01 | 0.22 | 0.00 | 1.06 | 0.00 | 0.08 | 0.01 | 0.08 | 0.00 | 0.00 | 0.02 | 0.19 | 0.08 | 0.47 | 0.04 | 0.08 | 0.04 | 0.15 | 0.09 | 0.20 | 0.13 | 0.09 | 0.04 | 0.05 | 0.02 | 0.00 | 0.00 | 0.07 | 0.00 | 0.03 | 0.02 | 0.07 | 0.02 | 0.09 | 0.07 | 0.06 |
| LGALS3 | ENSG00000131981 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.02 | 0.04 | 0.00 | 0.01 | 0.00 | 0.02 | 0.10 | 0.02 | 0.04 | 0.04 | 0.05 | 0.01 | 0.09 | 0.01 | 0.07 | 0.02 | 0.01 | 0.01 | 0.02 | 0.02 | 0.01 | 0.00 | 0.02 | 0.05 | 0.10 | 0.10 | 0.06 | 0.05 | 0.01 | 0.02 | 0.00 | 0.00 | 0.07 | 0.04 | 0.06 | 0.17 | 0.01 | 0.02 | 0.03 | 0.02 | 0.00 | 0.06 | 0.03 | 0.07 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.00 | 0.01 | 0.04 | 0.01 | 0.05 | 0.00 | 0.00 | 0.01 | 0.02 |
| PODNL1 | ENSG00000132000 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.02 | 0.05 | 0.00 | 0.00 | 0.09 | 0.02 | 0.01 | 0.05 | 0.13 | 0.04 | 0.07 | 0.02 | 0.14 | 0.05 | 0.07 | 0.02 | 0.03 | 0.00 | 0.02 | 0.01 | 0.01 | 0.02 | 0.08 | 0.06 | 0.00 | 0.03 | 0.21 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.10 | 0.03 | 0.89 | 0.06 | 0.11 | 0.01 | 0.24 | 0.01 | 0.25 | 0.11 | 0.24 | 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 | 0.02 | 0.02 |
| HSD17B7 | ENSG00000132196 | 0.03 | 0.00 | 0.01 | 0.00 | 0.00 | 0.03 | 0.01 | 0.04 | 0.74 | 0.01 | 0.02 | 0.00 | 0.10 | 0.02 | 0.23 | 0.00 | 0.26 | 0.00 | 0.05 | 0.00 | 0.21 | 0.01 | 0.12 | 0.00 | 0.03 | 0.00 | 0.13 | 0.00 | 0.06 | 0.00 | 0.30 | 0.00 | 0.30 | 0.01 | 0.10 | 0.02 | 0.04 | 0.00 | 0.00 | 0.00 | 0.26 | 0.01 | 0.38 | 0.02 | 0.16 | 0.00 | 0.14 | 0.00 | 0.31 | 0.00 | 0.34 | 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 |
| CNGA4 | ENSG00000132259 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.03 | 0.01 | 0.01 | 0.00 | 0.10 | 0.00 | 0.00 | 0.02 | 0.08 | 0.01 | 0.06 | 0.02 | 0.14 | 0.01 | 0.06 | 0.06 | 0.09 | 0.04 | 0.04 | 0.02 | 0.01 | 0.01 | 0.02 | 0.00 | 0.05 | 0.04 | 0.02 | 0.03 | 0.01 | 0.01 | 0.07 | 0.02 | 0.07 | 0.00 | 0.00 | 0.02 | 0.10 | 0.01 | 0.42 | 0.01 | 0.05 | 0.02 | 0.07 | 0.03 | 0.09 | 0.03 | 0.13 | 0.02 | 0.00 | 0.00 | 0.00 | 0.05 | 0.00 | 0.01 | 0.09 | 0.01 | 0.06 | 0.00 | 0.00 | 0.01 | 0.03 |
| RAMP1 | ENSG00000132329 | 0.01 | 0.08 | 0.04 | 0.05 | 0.00 | 0.05 | 0.01 | 0.04 | 0.00 | 0.30 | 0.00 | 0.00 | 0.00 | 0.08 | 0.04 | 0.05 | 0.03 | 0.19 | 0.01 | 0.18 | 0.04 | 0.16 | 0.03 | 0.08 | 0.02 | 0.03 | 0.04 | 0.03 | 0.04 | 0.04 | 0.03 | 0.08 | 0.00 | 0.01 | 0.03 | 0.05 | 0.00 | 0.01 | 0.00 | 0.01 | 0.03 | 0.10 | 0.20 | 0.26 | 0.01 | 0.38 | 0.03 | 0.06 | 0.16 | 0.09 | 0.05 | 0.39 | 0.03 | 0.05 | 0.00 | 0.00 | 0.13 | 0.00 | 0.00 | 0.12 | 0.00 | 0.03 | 0.01 | 0.08 | 0.02 | 0.15 |
| PTPRE | ENSG00000132334 | 0.00 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.06 | 0.03 | 0.09 | 0.00 | 0.02 | 0.02 | 0.15 | 0.03 | 0.05 | 0.05 | 0.06 | 0.02 | 0.04 | 0.06 | 0.06 | 0.10 | 0.07 | 0.01 | 0.05 | 0.02 | 0.04 | 0.03 | 0.01 | 0.02 | 0.10 | 0.14 | 0.17 | 0.11 | 0.02 | 0.02 | 0.02 | 0.00 | 0.00 | 0.05 | 0.10 | 0.25 | 0.18 | 0.03 | 0.05 | 0.06 | 0.06 | 0.09 | 0.04 | 0.07 | 0.05 | 0.05 | 0.08 | 0.00 | 0.00 | 0.03 | 0.03 | 0.01 | 0.13 | 0.00 | 0.07 | 0.00 | 0.00 | 0.01 | 0.04 |
| PRKAA1 | ENSG00000132356 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.02 | 0.01 | 0.13 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.22 | 0.01 | 0.22 | 0.00 | 0.10 | 0.00 | 0.22 | 0.01 | 0.20 | 0.01 | 0.05 | 0.01 | 0.05 | 0.00 | 0.03 | 0.00 | 0.04 | 0.00 | 0.00 | 0.01 | 0.22 | 0.00 | 0.03 | 0.01 | 0.00 | 0.00 | 0.06 | 0.02 | 0.23 | 0.02 | 0.06 | 0.00 | 0.07 | 0.01 | 0.16 | 0.03 | 0.26 | 0.02 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.13 | 0.02 |
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