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 |
| MAMDC2 | ENSG00000165072 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.03 | 0.05 | 0.00 | 0.01 | 0.03 | 0.05 | 0.01 | 0.05 | 0.05 | 0.05 | 0.01 | 0.03 | 0.08 | 0.03 | 0.04 | 0.05 | 0.01 | 0.01 | 0.03 | 0.02 | 0.00 | 0.00 | 0.02 | 0.03 | 0.00 | 0.15 | 0.05 | 0.02 | 0.00 | 0.02 | 0.00 | 0.00 | 0.04 | 0.05 | 0.10 | 0.15 | 0.01 | 0.03 | 0.02 | 0.03 | 0.00 | 0.11 | 0.17 | 0.02 | 0.03 | 0.02 | 0.00 | 0.02 | 0.00 | 0.04 | 0.00 | 0.01 | 0.01 | 0.04 | 0.00 | 0.00 | 0.03 | 0.04 |
| IL18RAP | ENSG00000115607 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.01 | 0.09 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.03 | 0.02 | 0.10 | 0.01 | 0.07 | 0.01 | 0.20 | 0.02 | 0.08 | 0.02 | 0.00 | 0.01 | 0.02 | 0.00 | 0.01 | 0.01 | 0.02 | 0.01 | 0.00 | 0.01 | 0.03 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.02 | 0.16 | 0.07 | 0.03 | 0.01 | 0.05 | 0.01 | 0.09 | 0.00 | 0.13 | 0.04 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 |
| PLA2G6 | ENSG00000184381 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.09 | 0.05 | 0.00 | 0.05 | 0.00 | 0.03 | 0.09 | 0.03 | 0.10 | 0.02 | 0.03 | 0.01 | 0.05 | 0.02 | 0.02 | 0.01 | 0.01 | 0.02 | 0.02 | 0.01 | 0.02 | 0.02 | 0.08 | 0.00 | 0.00 | 0.01 | 0.08 | 0.01 | 0.00 | 0.04 | 0.00 | 0.00 | 0.04 | 0.03 | 0.13 | 0.11 | 0.03 | 0.02 | 0.10 | 0.02 | 0.30 | 0.10 | 0.06 | 0.04 | 0.01 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.02 | 0.04 | 0.02 | 0.00 | 0.24 | 0.01 |
| ATP7A | ENSG00000165240 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.07 | 0.00 | 0.00 | 0.02 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.02 | 0.04 | 0.03 | 0.03 | 0.01 | 0.07 | 0.03 | 0.05 | 0.03 | 0.01 | 0.01 | 0.01 | 0.04 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.03 | 0.05 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.02 | 0.11 | 0.04 | 0.03 | 0.01 | 0.02 | 0.01 | 0.08 | 0.05 | 0.17 | 0.10 | 0.00 | 0.03 | 0.00 | 0.00 | 0.01 | 0.02 | 0.02 | 0.04 | 0.01 | 0.01 | 0.00 | 0.00 | 0.03 | 0.01 |
| TACR1 | ENSG00000115353 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.03 | 0.11 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.02 | 0.01 | 0.13 | 0.00 | 0.04 | 0.01 | 0.05 | 0.01 | 0.03 | 0.01 | 0.01 | 0.01 | 0.01 | 0.01 | 0.00 | 0.01 | 0.01 | 0.02 | 0.00 | 0.02 | 0.03 | 0.03 | 0.00 | 0.01 | 0.00 | 0.00 | 0.06 | 0.01 | 0.13 | 0.04 | 0.04 | 0.00 | 0.04 | 0.01 | 0.10 | 0.03 | 0.07 | 0.04 | 0.05 | 0.05 | 0.00 | 0.00 | 0.04 | 0.02 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.02 |
| MALT1 | ENSG00000172175 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.09 | 0.03 | 0.07 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.10 | 0.04 | 0.07 | 0.01 | 0.14 | 0.03 | 0.20 | 0.01 | 0.17 | 0.00 | 0.10 | 0.00 | 0.10 | 0.00 | 0.08 | 0.02 | 0.06 | 0.00 | 0.10 | 0.01 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.05 | 0.05 | 0.32 | 0.00 | 0.04 | 0.04 | 0.06 | 0.21 | 0.11 | 0.11 | 0.07 | 0.00 | 0.05 | 0.00 | 0.00 | 0.08 | 0.00 | 0.01 | 0.03 | 0.01 | 0.03 | 0.00 | 0.01 | 0.02 | 0.02 |
| GPC5 | ENSG00000179399 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.10 | 0.15 | 0.05 | 0.00 | 0.02 | 0.01 | 0.02 | 0.11 | 0.05 | 0.11 | 0.06 | 0.07 | 0.04 | 0.08 | 0.08 | 0.14 | 0.03 | 0.09 | 0.01 | 0.13 | 0.01 | 0.02 | 0.04 | 0.23 | 0.06 | 0.06 | 0.03 | 0.03 | 0.07 | 0.00 | 0.03 | 0.00 | 0.00 | 0.12 | 0.04 | 0.20 | 0.11 | 0.17 | 0.05 | 0.04 | 0.02 | 0.66 | 0.05 | 0.21 | 0.14 | 0.01 | 0.04 | 0.05 | 0.01 | 0.08 | 0.04 | 0.02 | 0.04 | 0.02 | 0.07 | 0.05 | 0.00 | 0.11 | 0.03 |
| NTN1 | ENSG00000065320 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.12 | 0.03 | 0.05 | 0.00 | 0.01 | 0.00 | 0.02 | 0.00 | 0.06 | 0.03 | 0.03 | 0.02 | 0.02 | 0.03 | 0.06 | 0.01 | 0.02 | 0.01 | 0.01 | 0.00 | 0.03 | 0.00 | 0.02 | 0.00 | 0.15 | 0.03 | 0.06 | 0.01 | 0.05 | 0.00 | 0.03 | 0.00 | 0.00 | 0.01 | 0.07 | 0.05 | 0.12 | 0.00 | 0.05 | 0.05 | 0.05 | 0.06 | 0.29 | 0.37 | 0.18 | 0.00 | 0.02 | 0.02 | 0.00 | 0.00 | 0.10 | 0.00 | 0.01 | 0.00 | 0.04 | 0.00 | 0.00 | 0.01 | 0.04 |
| USP7 | ENSG00000187555 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.29 | 0.05 | 0.00 | 0.00 | 0.06 | 0.00 | 0.05 | 0.02 | 0.06 | 0.05 | 0.05 | 0.01 | 0.07 | 0.04 | 0.06 | 0.04 | 0.00 | 0.02 | 0.00 | 0.02 | 0.01 | 0.00 | 0.02 | 0.01 | 0.00 | 0.05 | 0.06 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.07 | 0.02 | 0.14 | 0.14 | 0.16 | 0.01 | 0.03 | 0.02 | 0.06 | 0.05 | 0.12 | 0.02 | 0.02 | 0.00 | 0.00 | 0.00 | 0.05 | 0.04 | 0.01 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.04 | 0.01 |
| EZH1 | ENSG00000108799 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.09 | 0.04 | 0.02 | 0.01 | 0.01 | 0.01 | 0.02 | 0.06 | 0.01 | 0.02 | 0.05 | 0.03 | 0.01 | 0.13 | 0.02 | 0.11 | 0.03 | 0.04 | 0.01 | 0.03 | 0.03 | 0.03 | 0.03 | 0.05 | 0.03 | 0.02 | 0.01 | 0.01 | 0.14 | 0.01 | 0.12 | 0.00 | 0.00 | 0.05 | 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 |
| SLC8A2 | ENSG00000118160 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.05 | 0.06 | 0.04 | 0.00 | 0.02 | 0.00 | 0.09 | 0.02 | 0.08 | 0.04 | 0.12 | 0.02 | 0.02 | 0.05 | 0.04 | 0.06 | 0.02 | 0.01 | 0.03 | 0.01 | 0.04 | 0.03 | 0.05 | 0.03 | 0.04 | 0.00 | 0.10 | 0.13 | 0.03 | 0.00 | 0.03 | 0.00 | 0.00 | 0.05 | 0.06 | 0.03 | 0.33 | 0.05 | 0.08 | 0.04 | 0.06 | 0.06 | 0.19 | 0.02 | 0.20 | 0.00 | 0.04 | 0.01 | 0.00 | 0.07 | 0.03 | 0.00 | 0.13 | 0.03 | 0.13 | 0.03 | 0.00 | 0.02 | 0.04 |
| CNTNAP2 | ENSG00000174469 | 0.02 | 0.01 | 0.07 | 0.00 | 0.05 | 0.02 | 0.03 | 0.04 | 0.04 | 0.06 | 0.00 | 0.01 | 0.04 | 0.08 | 0.10 | 0.04 | 0.09 | 0.08 | 0.03 | 0.16 | 0.04 | 0.24 | 0.04 | 0.11 | 0.02 | 0.02 | 0.01 | 0.02 | 0.06 | 0.05 | 0.07 | 0.06 | 0.00 | 0.11 | 0.03 | 0.07 | 0.00 | 0.02 | 0.00 | 0.00 | 0.08 | 0.07 | 0.55 | 0.10 | 0.04 | 0.10 | 0.06 | 0.06 | 0.07 | 0.23 | 0.14 | 0.14 | 0.02 | 0.08 | 0.00 | 0.07 | 0.02 | 0.16 | 0.12 | 0.01 | 0.05 | 0.02 | 0.00 | 0.03 | 0.22 | 0.03 |
| PDE3B | ENSG00000152270 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.03 | 0.01 | 0.01 | 0.03 | 0.10 | 0.00 | 0.00 | 0.05 | 0.01 | 0.04 | 0.03 | 0.16 | 0.09 | 0.04 | 0.04 | 0.05 | 0.04 | 0.03 | 0.02 | 0.02 | 0.01 | 0.01 | 0.01 | 0.03 | 0.03 | 0.03 | 0.03 | 0.00 | 0.03 | 0.00 | 0.02 | 0.06 | 0.04 | 0.00 | 0.00 | 0.06 | 0.06 | 0.05 | 0.27 | 0.01 | 0.04 | 0.07 | 0.04 | 0.10 | 0.04 | 0.08 | 0.09 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.04 | 0.01 | 0.02 | 0.00 | 0.00 | 0.03 | 0.01 |
| FKBP7 | ENSG00000079150 | 0.02 | 0.01 | 0.08 | 0.00 | 0.00 | 0.00 | 0.01 | 0.07 | 0.06 | 0.05 | 0.00 | 0.00 | 0.00 | 0.02 | 0.05 | 0.01 | 0.20 | 0.02 | 0.15 | 0.01 | 0.17 | 0.02 | 0.05 | 0.04 | 0.01 | 0.01 | 0.03 | 0.02 | 0.03 | 0.01 | 0.07 | 0.04 | 0.05 | 0.01 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.02 | 0.42 | 0.05 | 0.13 | 0.02 | 0.06 | 0.01 | 0.03 | 0.00 | 0.02 | 0.10 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.02 |
| L3MBTL4 | ENSG00000154655 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.01 | 0.01 | 0.02 | 0.04 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.03 | 0.08 | 0.01 | 0.10 | 0.02 | 0.13 | 0.07 | 0.02 | 0.03 | 0.01 | 0.05 | 0.01 | 0.03 | 0.01 | 0.02 | 0.01 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.05 | 0.11 | 0.09 | 0.08 | 0.02 | 0.03 | 0.01 | 0.06 | 0.02 | 0.14 | 0.05 | 0.00 | 0.08 | 0.00 | 0.01 | 0.00 | 0.04 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.01 | 0.01 |
| FBLN5 | ENSG00000140092 | 0.00 | 0.02 | 0.01 | 0.01 | 0.00 | 0.04 | 0.01 | 0.06 | 0.07 | 0.06 | 0.00 | 0.00 | 0.00 | 0.07 | 0.05 | 0.05 | 0.11 | 0.02 | 0.04 | 0.05 | 0.08 | 0.06 | 0.04 | 0.04 | 0.00 | 0.03 | 0.01 | 0.02 | 0.02 | 0.01 | 0.01 | 0.10 | 0.00 | 0.31 | 0.05 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.04 | 0.09 | 0.20 | 0.17 | 0.07 | 0.09 | 0.04 | 0.03 | 0.06 | 0.02 | 0.06 | 0.10 | 0.03 | 0.01 | 0.00 | 0.00 | 0.03 | 0.00 | 0.00 | 0.10 | 0.02 | 0.06 | 0.03 | 0.01 | 0.01 | 0.06 |
| SLC35G2 | ENSG00000168917 | 0.03 | 0.01 | 0.00 | 0.01 | 0.03 | 0.00 | 0.08 | 0.01 | 0.07 | 0.02 | 0.00 | 0.01 | 0.00 | 0.03 | 0.06 | 0.01 | 0.30 | 0.01 | 0.24 | 0.00 | 0.25 | 0.02 | 0.11 | 0.01 | 0.01 | 0.01 | 0.02 | 0.01 | 0.00 | 0.00 | 0.04 | 0.01 | 0.00 | 0.03 | 0.06 | 0.02 | 0.00 | 0.06 | 0.00 | 0.00 | 0.08 | 0.03 | 0.45 | 0.03 | 0.23 | 0.00 | 0.08 | 0.01 | 0.19 | 0.02 | 0.06 | 0.07 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.02 | 0.01 | 0.02 | 0.02 | 0.04 | 0.00 | 0.00 | 0.01 | 0.05 |
| TET3 | ENSG00000187605 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.04 | 0.11 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.03 | 0.01 | 0.13 | 0.00 | 0.05 | 0.00 | 0.07 | 0.01 | 0.03 | 0.01 | 0.00 | 0.01 | 0.01 | 0.01 | 0.00 | 0.01 | 0.01 | 0.02 | 0.00 | 0.02 | 0.03 | 0.07 | 0.00 | 0.01 | 0.00 | 0.00 | 0.06 | 0.02 | 0.16 | 0.04 | 0.03 | 0.01 | 0.06 | 0.01 | 0.10 | 0.02 | 0.06 | 0.04 | 0.04 | 0.04 | 0.00 | 0.00 | 0.04 | 0.06 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.01 |
| FETUB | ENSG00000090512 | 0.05 | 0.00 | 0.03 | 0.01 | 0.00 | 0.01 | 0.03 | 0.04 | 0.19 | 0.01 | 0.00 | 0.00 | 0.00 | 0.07 | 0.14 | 0.05 | 1.57 | 0.00 | 0.61 | 0.00 | 0.70 | 0.02 | 0.22 | 0.01 | 0.04 | 0.01 | 0.06 | 0.02 | 0.03 | 0.00 | 0.12 | 0.02 | 0.12 | 0.03 | 0.10 | 0.00 | 0.00 | 0.10 | 0.00 | 0.00 | 0.18 | 0.02 | 1.06 | 0.04 | 0.62 | 0.00 | 0.33 | 0.01 | 0.78 | 0.09 | 0.12 | 0.09 | 0.24 | 0.00 | 0.00 | 0.00 | 0.06 | 0.00 | 0.02 | 0.02 | 0.12 | 0.05 | 0.00 | 0.00 | 0.03 | 0.04 |
| HDAC11 | ENSG00000163517 | 0.00 | 0.18 | 0.00 | 0.01 | 0.07 | 0.00 | 0.01 | 0.02 | 0.46 | 0.01 | 0.00 | 0.03 | 0.03 | 0.07 | 0.03 | 0.05 | 0.02 | 0.03 | 0.03 | 0.02 | 0.05 | 0.02 | 0.05 | 0.05 | 0.01 | 0.03 | 0.03 | 0.06 | 0.01 | 0.02 | 0.06 | 0.01 | 0.00 | 0.18 | 0.08 | 0.01 | 0.00 | 0.04 | 0.00 | 0.00 | 0.12 | 0.03 | 0.15 | 0.22 | 0.04 | 0.01 | 0.14 | 0.04 | 0.35 | 0.14 | 0.25 | 0.01 | 0.04 | 0.05 | 0.00 | 0.00 | 0.00 | 0.05 | 0.03 | 0.01 | 0.01 | 0.02 | 0.00 | 0.00 | 0.02 | 0.05 |
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