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 |
| SUPT16H | ENSG00000092201 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.03 | 0.08 | 0.06 | 0.00 | 0.00 | 0.00 | 0.05 | 0.14 | 0.02 | 0.14 | 0.08 | 0.09 | 0.07 | 0.09 | 0.07 | 0.09 | 0.05 | 0.03 | 0.02 | 0.01 | 0.08 | 0.02 | 0.05 | 0.08 | 0.00 | 0.00 | 0.02 | 0.29 | 0.03 | 0.01 | 0.02 | 0.00 | 0.00 | 0.09 | 0.03 | 0.40 | 0.10 | 0.08 | 0.01 | 0.07 | 0.04 | 0.16 | 0.10 | 0.17 | 0.08 | 0.02 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.03 | 0.01 | 0.10 | 0.00 | 0.00 | 0.03 | 0.02 |
| ASH1L | ENSG00000116539 | 0.03 | 0.00 | 0.01 | 0.00 | 0.00 | 0.03 | 0.05 | 0.03 | 0.36 | 0.01 | 0.02 | 0.00 | 0.11 | 0.00 | 0.37 | 0.00 | 0.26 | 0.00 | 0.05 | 0.01 | 0.20 | 0.00 | 0.16 | 0.01 | 0.03 | 0.00 | 0.11 | 0.00 | 0.09 | 0.00 | 0.37 | 0.00 | 0.58 | 0.01 | 0.16 | 0.02 | 0.06 | 0.00 | 0.00 | 0.00 | 0.34 | 0.01 | 0.57 | 0.02 | 0.19 | 0.01 | 0.23 | 0.00 | 0.96 | 0.01 | 0.41 | 0.01 | 0.09 | 0.00 | 0.00 | 0.00 | 0.25 | 0.00 | 0.02 | 0.00 | 0.07 | 0.00 | 0.00 | 0.00 | 0.21 | 0.00 |
| SAE1 | ENSG00000142230 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.05 | 0.06 | 0.04 | 0.00 | 0.02 | 0.00 | 0.09 | 0.01 | 0.08 | 0.04 | 0.11 | 0.02 | 0.02 | 0.06 | 0.04 | 0.06 | 0.03 | 0.01 | 0.03 | 0.03 | 0.04 | 0.02 | 0.04 | 0.03 | 0.05 | 0.00 | 0.10 | 0.13 | 0.04 | 0.00 | 0.03 | 0.00 | 0.00 | 0.04 | 0.07 | 0.03 | 0.33 | 0.05 | 0.08 | 0.04 | 0.06 | 0.06 | 0.19 | 0.04 | 0.20 | 0.00 | 0.04 | 0.01 | 0.00 | 0.21 | 0.03 | 0.00 | 0.13 | 0.02 | 0.13 | 0.00 | 0.00 | 0.02 | 0.03 |
| SP110 | ENSG00000135899 | 0.01 | 0.07 | 0.04 | 0.04 | 0.00 | 0.05 | 0.01 | 0.03 | 0.00 | 0.31 | 0.00 | 0.03 | 0.00 | 0.07 | 0.03 | 0.04 | 0.02 | 0.19 | 0.01 | 0.18 | 0.04 | 0.15 | 0.03 | 0.04 | 0.02 | 0.03 | 0.02 | 0.02 | 0.07 | 0.01 | 0.03 | 0.05 | 0.00 | 0.04 | 0.03 | 0.05 | 0.00 | 0.01 | 0.00 | 0.01 | 0.02 | 0.09 | 0.14 | 0.20 | 0.01 | 0.36 | 0.03 | 0.05 | 0.13 | 0.06 | 0.04 | 0.34 | 0.05 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.06 | 0.00 | 0.01 | 0.04 | 0.05 | 0.01 | 0.08 |
| CD8B | ENSG00000172116 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.04 | 0.07 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.02 | 0.02 | 0.10 | 0.01 | 0.06 | 0.02 | 0.10 | 0.01 | 0.03 | 0.01 | 0.00 | 0.01 | 0.01 | 0.02 | 0.00 | 0.01 | 0.02 | 0.02 | 0.00 | 0.02 | 0.04 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.04 | 0.02 | 0.11 | 0.04 | 0.05 | 0.01 | 0.03 | 0.02 | 0.09 | 0.03 | 0.21 | 0.04 | 0.01 | 0.04 | 0.00 | 0.00 | 0.04 | 0.04 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.02 |
| BCR | ENSG00000186716 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.02 | 0.20 | 0.04 | 0.02 | 0.01 | 0.01 | 0.05 | 0.10 | 0.03 | 0.18 | 0.03 | 0.05 | 0.01 | 0.07 | 0.02 | 0.04 | 0.02 | 0.02 | 0.01 | 0.05 | 0.05 | 0.00 | 0.04 | 0.01 | 0.04 | 0.03 | 0.05 | 0.04 | 0.06 | 0.00 | 0.01 | 0.00 | 0.00 | 0.06 | 0.04 | 0.19 | 0.08 | 0.02 | 0.00 | 0.07 | 0.03 | 0.39 | 0.03 | 0.14 | 0.05 | 0.22 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.01 | 0.03 | 0.00 | 0.00 | 0.10 | 0.03 |
| PRMT1 | ENSG00000126457 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.01 | 0.10 | 0.03 | 0.00 | 0.02 | 0.00 | 0.06 | 0.01 | 0.07 | 0.05 | 0.10 | 0.03 | 0.02 | 0.07 | 0.05 | 0.08 | 0.03 | 0.01 | 0.03 | 0.01 | 0.03 | 0.03 | 0.05 | 0.03 | 0.03 | 0.00 | 0.07 | 0.25 | 0.02 | 0.00 | 0.03 | 0.00 | 0.00 | 0.12 | 0.04 | 0.05 | 0.32 | 0.05 | 0.07 | 0.06 | 0.05 | 0.18 | 0.15 | 0.03 | 0.18 | 0.00 | 0.04 | 0.01 | 0.00 | 0.07 | 0.03 | 0.00 | 0.14 | 0.03 | 0.13 | 0.00 | 0.00 | 0.02 | 0.03 |
| BDH1 | ENSG00000161267 | 0.05 | 0.00 | 0.03 | 0.01 | 0.00 | 0.01 | 0.03 | 0.06 | 0.19 | 0.01 | 0.00 | 0.00 | 0.00 | 0.06 | 0.14 | 0.06 | 1.37 | 0.01 | 0.59 | 0.00 | 0.79 | 0.02 | 0.25 | 0.03 | 0.05 | 0.01 | 0.06 | 0.02 | 0.03 | 0.01 | 0.12 | 0.03 | 0.12 | 0.03 | 0.10 | 0.04 | 0.00 | 0.10 | 0.00 | 0.00 | 0.22 | 0.03 | 1.02 | 0.09 | 0.65 | 0.00 | 0.39 | 0.01 | 0.72 | 0.17 | 0.10 | 0.13 | 0.11 | 0.04 | 0.00 | 0.00 | 0.35 | 0.05 | 0.02 | 0.07 | 0.09 | 0.07 | 0.00 | 0.00 | 0.04 | 0.04 |
| TRRAP | ENSG00000196367 | 0.01 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.06 | 0.02 | 0.07 | 0.01 | 0.00 | 0.00 | 0.03 | 0.00 | 0.11 | 0.02 | 0.25 | 0.01 | 0.25 | 0.00 | 0.62 | 0.02 | 0.38 | 0.01 | 0.02 | 0.00 | 0.02 | 0.00 | 0.17 | 0.01 | 0.09 | 0.02 | 0.11 | 0.01 | 0.07 | 0.03 | 0.00 | 0.02 | 0.00 | 0.00 | 0.07 | 0.04 | 0.21 | 0.05 | 0.07 | 0.01 | 0.06 | 0.01 | 0.08 | 0.04 | 0.09 | 0.04 | 0.09 | 0.01 | 0.00 | 0.00 | 0.13 | 0.00 | 0.05 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.05 | 0.03 |
| BCAN | ENSG00000132692 | 0.03 | 0.00 | 0.01 | 0.01 | 0.00 | 0.03 | 0.01 | 0.03 | 0.32 | 0.01 | 0.02 | 0.00 | 0.11 | 0.00 | 0.31 | 0.00 | 0.24 | 0.00 | 0.05 | 0.01 | 0.25 | 0.00 | 0.14 | 0.00 | 0.04 | 0.00 | 0.11 | 0.00 | 0.07 | 0.00 | 0.32 | 0.00 | 0.43 | 0.01 | 0.09 | 0.02 | 0.06 | 0.00 | 0.00 | 0.00 | 0.28 | 0.01 | 0.44 | 0.02 | 0.16 | 0.00 | 0.18 | 0.00 | 0.47 | 0.01 | 0.35 | 0.01 | 0.11 | 0.00 | 0.00 | 0.00 | 0.25 | 0.00 | 0.05 | 0.00 | 0.06 | 0.00 | 0.00 | 0.00 | 0.16 | 0.01 |
| TK1 | ENSG00000167900 | 0.02 | 0.00 | 0.05 | 0.00 | 0.02 | 0.00 | 0.04 | 0.04 | 0.20 | 0.00 | 0.00 | 0.02 | 0.09 | 0.02 | 0.19 | 0.01 | 0.21 | 0.03 | 0.07 | 0.04 | 0.21 | 0.07 | 0.10 | 0.03 | 0.05 | 0.00 | 0.05 | 0.03 | 0.04 | 0.09 | 0.26 | 0.02 | 0.08 | 0.01 | 0.08 | 0.02 | 0.02 | 0.01 | 0.00 | 0.00 | 0.37 | 0.03 | 0.41 | 0.03 | 0.12 | 0.06 | 0.14 | 0.01 | 0.59 | 0.02 | 0.22 | 0.02 | 0.05 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.07 | 0.00 | 0.05 | 0.01 | 0.15 | 0.00 | 0.25 | 0.01 |
| PRAME | ENSG00000185686 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.02 | 0.21 | 0.04 | 0.03 | 0.01 | 0.03 | 0.05 | 0.14 | 0.03 | 0.26 | 0.03 | 0.09 | 0.01 | 0.06 | 0.02 | 0.06 | 0.02 | 0.02 | 0.01 | 0.05 | 0.05 | 0.00 | 0.04 | 0.01 | 0.04 | 0.03 | 0.05 | 0.06 | 0.06 | 0.00 | 0.01 | 0.00 | 0.00 | 0.06 | 0.04 | 0.24 | 0.08 | 0.04 | 0.00 | 0.07 | 0.03 | 0.32 | 0.03 | 0.18 | 0.05 | 0.25 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.03 | 0.03 | 0.00 | 0.00 | 0.12 | 0.03 |
| COL1A1 | ENSG00000108821 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.13 | 0.01 | 0.00 | 0.00 | 0.09 | 0.00 | 0.10 | 0.00 | 0.12 | 0.01 | 0.02 | 0.01 | 0.16 | 0.01 | 0.10 | 0.01 | 0.03 | 0.01 | 0.06 | 0.04 | 0.07 | 0.02 | 0.05 | 0.01 | 0.02 | 0.01 | 0.05 | 0.03 | 0.01 | 0.03 | 0.00 | 0.00 | 0.51 | 0.02 | 0.17 | 0.04 | 0.06 | 0.00 | 0.06 | 0.03 | 0.15 | 0.02 | 0.09 | 0.03 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.02 | 0.01 | 0.03 | 0.03 | 0.12 | 0.01 |
| NEIL3 | ENSG00000109674 | 0.00 | 0.03 | 0.00 | 0.03 | 0.10 | 0.04 | 0.04 | 0.06 | 0.05 | 0.19 | 0.00 | 0.02 | 0.00 | 0.08 | 0.02 | 0.11 | 0.02 | 0.18 | 0.02 | 0.12 | 0.06 | 0.16 | 0.02 | 0.17 | 0.02 | 0.10 | 0.02 | 0.08 | 0.00 | 0.05 | 0.06 | 0.18 | 0.00 | 0.39 | 0.10 | 0.11 | 0.00 | 0.04 | 0.00 | 0.01 | 0.04 | 0.11 | 0.07 | 0.38 | 0.04 | 0.10 | 0.01 | 0.08 | 0.11 | 0.16 | 0.03 | 0.24 | 0.02 | 0.00 | 0.00 | 0.00 | 0.03 | 0.09 | 0.01 | 0.10 | 0.00 | 0.08 | 0.00 | 0.00 | 0.04 | 0.08 |
| LONP1 | ENSG00000196365 | 0.00 | 0.01 | 0.00 | 0.02 | 0.00 | 0.04 | 0.01 | 0.03 | 0.03 | 0.10 | 0.00 | 0.03 | 0.01 | 0.09 | 0.01 | 0.06 | 0.05 | 0.09 | 0.05 | 0.10 | 0.04 | 0.11 | 0.02 | 0.07 | 0.02 | 0.03 | 0.01 | 0.08 | 0.00 | 0.06 | 0.01 | 0.12 | 0.00 | 0.01 | 0.01 | 0.03 | 0.01 | 0.00 | 0.00 | 0.00 | 0.07 | 0.08 | 0.12 | 0.64 | 0.03 | 0.18 | 0.01 | 0.23 | 0.02 | 0.56 | 0.23 | 0.05 | 0.02 | 0.00 | 0.00 | 0.01 | 0.00 | 0.03 | 0.01 | 0.01 | 0.04 | 0.01 | 0.00 | 0.05 | 0.05 | 0.04 |
| MAP2K1 | ENSG00000169032 | 0.01 | 0.00 | 0.00 | 0.00 | 0.05 | 0.00 | 0.01 | 0.02 | 0.02 | 0.02 | 0.00 | 0.00 | 0.09 | 0.00 | 0.03 | 0.02 | 0.04 | 0.03 | 0.02 | 0.02 | 0.04 | 0.02 | 0.05 | 0.03 | 0.01 | 0.01 | 0.01 | 0.01 | 0.03 | 0.02 | 0.03 | 0.01 | 0.00 | 0.01 | 0.04 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.07 | 0.05 | 0.13 | 0.10 | 0.06 | 0.01 | 0.01 | 0.04 | 0.00 | 0.17 | 0.11 | 0.03 | 0.01 | 0.02 | 0.00 | 0.00 | 0.06 | 0.02 | 0.01 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.06 | 0.00 |
| LMNA | ENSG00000160789 | 0.03 | 0.00 | 0.01 | 0.00 | 0.00 | 0.03 | 0.02 | 0.03 | 0.37 | 0.01 | 0.02 | 0.00 | 0.11 | 0.00 | 0.32 | 0.00 | 0.23 | 0.00 | 0.05 | 0.01 | 0.24 | 0.00 | 0.16 | 0.01 | 0.03 | 0.00 | 0.11 | 0.00 | 0.07 | 0.00 | 0.35 | 0.00 | 0.48 | 0.01 | 0.09 | 0.02 | 0.07 | 0.00 | 0.00 | 0.00 | 0.28 | 0.01 | 0.57 | 0.02 | 0.19 | 0.00 | 0.33 | 0.00 | 1.07 | 0.01 | 0.32 | 0.02 | 0.10 | 0.00 | 0.00 | 0.00 | 0.25 | 0.00 | 0.05 | 0.00 | 0.05 | 0.00 | 0.00 | 0.00 | 0.18 | 0.01 |
| PKLR | ENSG00000143627 | 0.03 | 0.00 | 0.01 | 0.01 | 0.00 | 0.03 | 0.08 | 0.01 | 0.36 | 0.02 | 0.02 | 0.00 | 0.11 | 0.00 | 0.37 | 0.00 | 0.26 | 0.00 | 0.05 | 0.01 | 0.20 | 0.00 | 0.16 | 0.00 | 0.03 | 0.00 | 0.11 | 0.00 | 0.09 | 0.00 | 0.38 | 0.00 | 0.58 | 0.01 | 0.18 | 0.02 | 0.06 | 0.00 | 0.00 | 0.00 | 0.34 | 0.00 | 0.58 | 0.02 | 0.19 | 0.00 | 0.24 | 0.00 | 1.03 | 0.01 | 0.36 | 0.01 | 0.09 | 0.00 | 0.00 | 0.00 | 0.25 | 0.00 | 0.02 | 0.00 | 0.07 | 0.00 | 0.00 | 0.00 | 0.19 | 0.00 |
| RET | ENSG00000165731 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.03 | 0.08 | 0.05 | 0.00 | 0.00 | 0.01 | 0.04 | 0.05 | 0.01 | 0.13 | 0.01 | 0.06 | 0.02 | 0.07 | 0.05 | 0.05 | 0.01 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.01 | 0.03 | 0.01 | 0.15 | 0.01 | 0.08 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.07 | 0.03 | 0.08 | 0.10 | 0.01 | 0.03 | 0.01 | 0.03 | 0.05 | 0.03 | 0.11 | 0.07 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 |
| BACE2 | ENSG00000182240 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.30 | 0.04 | 0.04 | 0.00 | 0.03 | 0.00 | 0.00 | 0.02 | 0.03 | 0.05 | 0.08 | 0.02 | 0.06 | 0.02 | 0.10 | 0.03 | 0.07 | 0.01 | 0.01 | 0.01 | 0.07 | 0.01 | 0.01 | 0.02 | 0.01 | 0.07 | 0.03 | 0.01 | 0.04 | 0.02 | 0.00 | 0.00 | 0.00 | 0.09 | 0.02 | 0.12 | 0.16 | 0.05 | 0.03 | 0.04 | 0.02 | 0.04 | 0.03 | 0.07 | 0.06 | 0.04 | 0.00 | 0.12 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.03 | 0.00 | 0.01 | 0.03 |
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