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 |
| COMP | ENSG00000105664 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.03 | 0.01 | 0.03 | 0.07 | 0.00 | 0.03 | 0.03 | 0.12 | 0.02 | 0.04 | 0.02 | 0.13 | 0.01 | 0.04 | 0.02 | 0.00 | 0.00 | 0.01 | 0.04 | 0.02 | 0.02 | 0.08 | 0.02 | 0.06 | 0.03 | 0.21 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.09 | 0.02 | 0.49 | 0.06 | 0.02 | 0.02 | 0.16 | 0.04 | 0.43 | 0.07 | 0.07 | 0.04 | 0.01 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.02 | 0.00 | 0.01 | 0.01 | 0.02 | 0.00 | 0.03 | 0.01 |
| GAPDHS | ENSG00000105679 | 0.00 | 0.00 | 0.03 | 0.00 | 0.00 | 0.02 | 0.01 | 0.01 | 0.19 | 0.02 | 0.00 | 0.00 | 0.07 | 0.02 | 0.26 | 0.00 | 0.43 | 0.03 | 0.08 | 0.01 | 0.22 | 0.03 | 0.08 | 0.04 | 0.05 | 0.00 | 0.04 | 0.00 | 0.10 | 0.00 | 0.05 | 0.02 | 0.13 | 0.01 | 0.00 | 0.02 | 0.00 | 0.03 | 0.00 | 0.00 | 0.14 | 0.02 | 0.64 | 0.05 | 0.21 | 0.02 | 0.19 | 0.02 | 1.50 | 0.01 | 0.29 | 0.05 | 0.01 | 0.03 | 0.00 | 0.01 | 0.08 | 0.00 | 0.02 | 0.01 | 0.03 | 0.02 | 0.00 | 0.00 | 0.04 | 0.01 |
| MAG | ENSG00000105695 | 0.00 | 0.00 | 0.03 | 0.00 | 0.00 | 0.02 | 0.01 | 0.01 | 0.19 | 0.03 | 0.00 | 0.00 | 0.11 | 0.02 | 0.24 | 0.00 | 0.44 | 0.02 | 0.08 | 0.01 | 0.22 | 0.03 | 0.09 | 0.04 | 0.05 | 0.00 | 0.04 | 0.01 | 0.11 | 0.00 | 0.06 | 0.02 | 0.13 | 0.01 | 0.03 | 0.02 | 0.00 | 0.02 | 0.00 | 0.00 | 0.14 | 0.02 | 0.66 | 0.05 | 0.24 | 0.02 | 0.18 | 0.01 | 1.44 | 0.01 | 0.29 | 0.05 | 0.01 | 0.02 | 0.00 | 0.01 | 0.08 | 0.00 | 0.01 | 0.02 | 0.03 | 0.03 | 0.00 | 0.00 | 0.06 | 0.01 |
| HAMP | ENSG00000105697 | 0.00 | 0.00 | 0.03 | 0.00 | 0.00 | 0.02 | 0.01 | 0.01 | 0.18 | 0.02 | 0.00 | 0.00 | 0.11 | 0.02 | 0.25 | 0.00 | 0.44 | 0.02 | 0.08 | 0.01 | 0.22 | 0.03 | 0.09 | 0.04 | 0.05 | 0.00 | 0.04 | 0.01 | 0.11 | 0.00 | 0.06 | 0.02 | 0.13 | 0.01 | 0.03 | 0.02 | 0.00 | 0.02 | 0.00 | 0.00 | 0.15 | 0.02 | 0.68 | 0.05 | 0.21 | 0.02 | 0.18 | 0.01 | 1.44 | 0.01 | 0.29 | 0.05 | 0.01 | 0.02 | 0.00 | 0.01 | 0.08 | 0.00 | 0.01 | 0.02 | 0.03 | 0.03 | 0.00 | 0.00 | 0.06 | 0.01 |
| SCN1B | ENSG00000105711 | 0.00 | 0.00 | 0.03 | 0.00 | 0.00 | 0.02 | 0.01 | 0.01 | 0.18 | 0.02 | 0.00 | 0.00 | 0.11 | 0.02 | 0.26 | 0.01 | 0.41 | 0.02 | 0.08 | 0.01 | 0.22 | 0.04 | 0.12 | 0.04 | 0.07 | 0.00 | 0.04 | 0.01 | 0.11 | 0.01 | 0.07 | 0.02 | 0.13 | 0.03 | 0.01 | 0.02 | 0.00 | 0.02 | 0.01 | 0.00 | 0.14 | 0.01 | 0.68 | 0.04 | 0.17 | 0.02 | 0.19 | 0.01 | 1.44 | 0.00 | 0.28 | 0.05 | 0.01 | 0.02 | 0.00 | 0.01 | 0.08 | 0.00 | 0.01 | 0.02 | 0.03 | 0.03 | 0.00 | 0.00 | 0.06 | 0.02 |
| TFPI2 | ENSG00000105825 | 0.01 | 0.00 | 0.06 | 0.00 | 0.00 | 0.00 | 0.05 | 0.00 | 0.05 | 0.02 | 0.00 | 0.00 | 0.03 | 0.01 | 0.07 | 0.01 | 0.26 | 0.01 | 0.25 | 0.01 | 0.71 | 0.01 | 0.37 | 0.01 | 0.03 | 0.00 | 0.01 | 0.01 | 0.08 | 0.01 | 0.10 | 0.02 | 0.18 | 0.01 | 0.11 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.06 | 0.02 | 0.16 | 0.06 | 0.05 | 0.01 | 0.05 | 0.02 | 0.08 | 0.03 | 0.13 | 0.03 | 0.12 | 0.00 | 0.00 | 0.00 | 0.13 | 0.00 | 0.03 | 0.00 | 0.08 | 0.00 | 0.00 | 0.02 | 0.03 | 0.02 |
| NAMPT | ENSG00000105835 | 0.01 | 0.00 | 0.05 | 0.01 | 0.01 | 0.00 | 0.04 | 0.02 | 0.03 | 0.02 | 0.00 | 0.00 | 0.04 | 0.00 | 0.09 | 0.02 | 0.17 | 0.03 | 0.15 | 0.02 | 0.36 | 0.06 | 0.16 | 0.04 | 0.01 | 0.01 | 0.01 | 0.00 | 0.03 | 0.03 | 0.07 | 0.02 | 0.00 | 0.02 | 0.07 | 0.06 | 0.00 | 0.02 | 0.00 | 0.00 | 0.06 | 0.04 | 0.26 | 0.06 | 0.04 | 0.03 | 0.03 | 0.02 | 0.23 | 0.05 | 0.14 | 0.03 | 0.08 | 0.01 | 0.00 | 0.01 | 0.13 | 0.00 | 0.09 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.08 | 0.03 |
| PIK3CG | ENSG00000105851 | 0.01 | 0.00 | 0.05 | 0.01 | 0.01 | 0.00 | 0.05 | 0.02 | 0.05 | 0.02 | 0.00 | 0.00 | 0.03 | 0.00 | 0.09 | 0.02 | 0.15 | 0.03 | 0.16 | 0.02 | 0.35 | 0.07 | 0.15 | 0.04 | 0.01 | 0.01 | 0.01 | 0.00 | 0.04 | 0.02 | 0.08 | 0.02 | 0.00 | 0.02 | 0.02 | 0.06 | 0.00 | 0.02 | 0.00 | 0.00 | 0.05 | 0.04 | 0.25 | 0.06 | 0.04 | 0.03 | 0.03 | 0.03 | 0.05 | 0.05 | 0.14 | 0.02 | 0.08 | 0.01 | 0.00 | 0.01 | 0.13 | 0.00 | 0.09 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.08 | 0.03 |
| PON3 | ENSG00000105852 | 0.01 | 0.00 | 0.06 | 0.00 | 0.00 | 0.00 | 0.05 | 0.00 | 0.05 | 0.01 | 0.00 | 0.00 | 0.03 | 0.00 | 0.08 | 0.01 | 0.21 | 0.01 | 0.22 | 0.00 | 0.65 | 0.04 | 0.30 | 0.00 | 0.04 | 0.00 | 0.02 | 0.01 | 0.08 | 0.01 | 0.11 | 0.02 | 0.18 | 0.01 | 0.10 | 0.01 | 0.01 | 0.02 | 0.00 | 0.00 | 0.07 | 0.02 | 0.18 | 0.06 | 0.05 | 0.01 | 0.06 | 0.03 | 0.08 | 0.03 | 0.08 | 0.03 | 0.12 | 0.00 | 0.00 | 0.00 | 0.13 | 0.00 | 0.04 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.03 | 0.02 |
| PON2 | ENSG00000105854 | 0.01 | 0.00 | 0.06 | 0.00 | 0.00 | 0.00 | 0.05 | 0.00 | 0.05 | 0.01 | 0.00 | 0.00 | 0.03 | 0.00 | 0.08 | 0.01 | 0.21 | 0.01 | 0.22 | 0.00 | 0.65 | 0.04 | 0.30 | 0.00 | 0.04 | 0.00 | 0.02 | 0.01 | 0.08 | 0.01 | 0.13 | 0.02 | 0.18 | 0.01 | 0.12 | 0.01 | 0.01 | 0.02 | 0.00 | 0.00 | 0.07 | 0.02 | 0.18 | 0.06 | 0.05 | 0.02 | 0.06 | 0.03 | 0.15 | 0.03 | 0.08 | 0.03 | 0.12 | 0.00 | 0.00 | 0.00 | 0.13 | 0.00 | 0.04 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.03 | 0.02 |
| ITGB8 | ENSG00000105855 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.03 | 0.20 | 0.01 | 0.00 | 0.00 | 0.08 | 0.00 | 0.13 | 0.00 | 0.12 | 0.01 | 0.05 | 0.01 | 0.16 | 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 | 0.19 | 0.21 | 0.01 | 0.01 | 0.05 | 0.03 | 0.17 | 0.01 | 0.17 | 0.04 | 0.08 | 0.00 | 0.00 | 0.02 | 0.06 | 0.02 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.11 | 0.02 |
| NPVF | ENSG00000105954 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.01 | 0.08 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.07 | 0.00 | 0.08 | 0.02 | 0.05 | 0.01 | 0.19 | 0.01 | 0.08 | 0.01 | 0.05 | 0.00 | 0.03 | 0.01 | 0.04 | 0.00 | 0.07 | 0.00 | 0.00 | 0.01 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.08 | 0.02 | 0.16 | 0.18 | 0.04 | 0.00 | 0.07 | 0.03 | 0.09 | 0.01 | 0.16 | 0.04 | 0.06 | 0.00 | 0.00 | 0.01 | 0.00 | 0.02 | 0.01 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.09 | 0.02 |
| FKBP14 | ENSG00000106080 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.00 | 0.10 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.06 | 0.01 | 0.09 | 0.02 | 0.06 | 0.01 | 0.13 | 0.02 | 0.04 | 0.00 | 0.05 | 0.00 | 0.03 | 0.00 | 0.03 | 0.00 | 0.05 | 0.00 | 0.00 | 0.02 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.08 | 0.02 | 0.16 | 0.11 | 0.02 | 0.00 | 0.06 | 0.02 | 0.08 | 0.01 | 0.18 | 0.05 | 0.05 | 0.00 | 0.00 | 0.01 | 0.00 | 0.02 | 0.03 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.07 | 0.02 |
| STX1A | ENSG00000106089 | 0.02 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.05 | 0.02 | 0.00 | 0.00 | 0.02 | 0.00 | 0.02 | 0.02 | 0.08 | 0.02 | 0.04 | 0.03 | 0.18 | 0.03 | 0.09 | 0.02 | 0.01 | 0.01 | 0.01 | 0.00 | 0.02 | 0.00 | 0.08 | 0.01 | 0.00 | 0.01 | 0.15 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.09 | 0.02 | 0.16 | 0.06 | 0.04 | 0.01 | 0.07 | 0.02 | 0.22 | 0.00 | 0.07 | 0.03 | 0.12 | 0.00 | 0.00 | 0.00 | 0.10 | 0.00 | 0.01 | 0.01 | 0.06 | 0.00 | 0.00 | 0.00 | 0.06 | 0.02 |
| NOD1 | ENSG00000106100 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.05 | 0.00 | 0.13 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.06 | 0.01 | 0.08 | 0.02 | 0.04 | 0.01 | 0.14 | 0.03 | 0.04 | 0.00 | 0.04 | 0.00 | 0.04 | 0.00 | 0.02 | 0.00 | 0.05 | 0.00 | 0.00 | 0.02 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.09 | 0.02 | 0.16 | 0.12 | 0.02 | 0.00 | 0.05 | 0.02 | 0.04 | 0.01 | 0.17 | 0.05 | 0.05 | 0.00 | 0.00 | 0.01 | 0.00 | 0.02 | 0.02 | 0.00 | 0.06 | 0.00 | 0.00 | 0.00 | 0.07 | 0.02 |
| EPHB6 | ENSG00000106123 | 0.02 | 0.01 | 0.05 | 0.00 | 0.05 | 0.02 | 0.02 | 0.03 | 0.05 | 0.03 | 0.00 | 0.01 | 0.04 | 0.03 | 0.07 | 0.02 | 0.08 | 0.06 | 0.02 | 0.15 | 0.04 | 0.20 | 0.03 | 0.09 | 0.02 | 0.01 | 0.03 | 0.02 | 0.03 | 0.04 | 0.04 | 0.05 | 0.00 | 0.11 | 0.06 | 0.06 | 0.00 | 0.02 | 0.00 | 0.00 | 0.09 | 0.04 | 0.55 | 0.04 | 0.03 | 0.09 | 0.04 | 0.05 | 0.05 | 0.14 | 0.12 | 0.11 | 0.02 | 0.04 | 0.00 | 0.05 | 0.02 | 0.09 | 0.10 | 0.01 | 0.04 | 0.02 | 0.00 | 0.03 | 0.21 | 0.02 |
| GHRHR | ENSG00000106128 | 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 | 0.05 | 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 | 0.16 | 0.12 | 0.03 | 0.00 | 0.06 | 0.02 | 0.04 | 0.01 | 0.16 | 0.03 | 0.05 | 0.00 | 0.00 | 0.01 | 0.00 | 0.02 | 0.03 | 0.00 | 0.07 | 0.00 | 0.00 | 0.00 | 0.06 | 0.02 |
| CASP2 | ENSG00000106144 | 0.02 | 0.01 | 0.05 | 0.00 | 0.05 | 0.02 | 0.02 | 0.03 | 0.05 | 0.03 | 0.00 | 0.01 | 0.04 | 0.03 | 0.07 | 0.02 | 0.08 | 0.06 | 0.02 | 0.15 | 0.03 | 0.20 | 0.02 | 0.10 | 0.03 | 0.00 | 0.02 | 0.03 | 0.02 | 0.04 | 0.04 | 0.05 | 0.00 | 0.11 | 0.06 | 0.06 | 0.00 | 0.02 | 0.00 | 0.00 | 0.08 | 0.05 | 0.54 | 0.04 | 0.03 | 0.09 | 0.05 | 0.05 | 0.10 | 0.14 | 0.13 | 0.11 | 0.02 | 0.04 | 0.00 | 0.05 | 0.02 | 0.09 | 0.11 | 0.01 | 0.04 | 0.02 | 0.00 | 0.03 | 0.21 | 0.02 |
| CCL24 | ENSG00000106178 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.04 | 0.02 | 0.00 | 0.00 | 0.02 | 0.00 | 0.02 | 0.02 | 0.08 | 0.02 | 0.05 | 0.03 | 0.13 | 0.02 | 0.11 | 0.01 | 0.01 | 0.01 | 0.01 | 0.01 | 0.03 | 0.00 | 0.04 | 0.01 | 0.00 | 0.01 | 0.16 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.06 | 0.02 | 0.19 | 0.07 | 0.05 | 0.01 | 0.04 | 0.02 | 0.10 | 0.03 | 0.05 | 0.07 | 0.09 | 0.00 | 0.00 | 0.00 | 0.10 | 0.00 | 0.02 | 0.01 | 0.10 | 0.01 | 0.00 | 0.00 | 0.05 | 0.02 |
| NPTX2 | ENSG00000106236 | 0.01 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.05 | 0.02 | 0.06 | 0.01 | 0.00 | 0.00 | 0.03 | 0.00 | 0.12 | 0.01 | 0.25 | 0.01 | 0.24 | 0.00 | 0.60 | 0.02 | 0.38 | 0.01 | 0.03 | 0.00 | 0.01 | 0.00 | 0.16 | 0.01 | 0.08 | 0.02 | 0.11 | 0.01 | 0.10 | 0.03 | 0.00 | 0.02 | 0.00 | 0.00 | 0.06 | 0.03 | 0.19 | 0.06 | 0.05 | 0.01 | 0.05 | 0.01 | 0.08 | 0.04 | 0.08 | 0.04 | 0.10 | 0.00 | 0.00 | 0.00 | 0.13 | 0.00 | 0.05 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.05 | 0.02 |
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