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 |
| TGFBR1 | ENSG00000106799 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.02 | 0.08 | 0.00 | 0.01 | 0.02 | 0.06 | 0.01 | 0.03 | 0.04 | 0.01 | 0.04 | 0.00 | 0.09 | 0.01 | 0.02 | 0.05 | 0.01 | 0.01 | 0.04 | 0.03 | 0.00 | 0.04 | 0.01 | 0.05 | 0.00 | 0.08 | 0.08 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.03 | 0.05 | 0.06 | 0.14 | 0.02 | 0.02 | 0.01 | 0.04 | 0.00 | 0.20 | 0.11 | 0.03 | 0.04 | 0.02 | 0.00 | 0.02 | 0.00 | 0.03 | 0.01 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.01 | 0.02 |
| UGT1A10 | ENSG00000242515 | 0.01 | 0.08 | 0.04 | 0.05 | 0.00 | 0.05 | 0.01 | 0.04 | 0.01 | 0.34 | 0.00 | 0.04 | 0.00 | 0.08 | 0.03 | 0.05 | 0.02 | 0.20 | 0.01 | 0.19 | 0.05 | 0.16 | 0.03 | 0.08 | 0.02 | 0.03 | 0.02 | 0.02 | 0.04 | 0.03 | 0.03 | 0.06 | 0.00 | 0.01 | 0.00 | 0.07 | 0.00 | 0.01 | 0.00 | 0.01 | 0.02 | 0.10 | 0.17 | 0.23 | 0.01 | 0.39 | 0.03 | 0.06 | 0.13 | 0.06 | 0.04 | 0.40 | 0.04 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.12 | 0.00 | 0.05 | 0.01 | 0.08 | 0.01 | 0.12 |
| SLC38A9 | ENSG00000177058 | 0.00 | 0.00 | 0.00 | 0.01 | 0.03 | 0.00 | 0.01 | 0.22 | 0.06 | 0.13 | 0.00 | 0.00 | 0.01 | 0.01 | 0.07 | 0.06 | 0.04 | 0.10 | 0.03 | 0.08 | 0.03 | 0.14 | 0.02 | 0.10 | 0.02 | 0.06 | 0.01 | 0.06 | 0.00 | 0.05 | 0.04 | 0.01 | 0.00 | 0.10 | 0.09 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.03 | 0.10 | 0.04 | 0.53 | 0.04 | 0.07 | 0.01 | 0.12 | 0.01 | 0.31 | 0.11 | 0.05 | 0.00 | 0.02 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.04 | 0.03 |
| MYLK | ENSG00000065534 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.03 | 0.05 | 0.02 | 0.00 | 0.01 | 0.00 | 0.01 | 0.04 | 0.02 | 0.11 | 0.01 | 0.03 | 0.00 | 0.08 | 0.04 | 0.05 | 0.01 | 0.00 | 0.00 | 0.03 | 0.01 | 0.00 | 0.00 | 0.02 | 0.02 | 0.00 | 0.05 | 0.03 | 0.01 | 0.00 | 0.05 | 0.00 | 0.00 | 0.03 | 0.04 | 0.23 | 0.05 | 0.08 | 0.01 | 0.08 | 0.01 | 0.07 | 0.09 | 0.11 | 0.07 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.03 | 0.01 | 0.07 | 0.00 | 0.00 | 0.00 | 0.04 |
| COLQ | ENSG00000206561 | 0.00 | 0.18 | 0.00 | 0.01 | 0.07 | 0.00 | 0.01 | 0.02 | 0.27 | 0.02 | 0.00 | 0.03 | 0.01 | 0.05 | 0.03 | 0.04 | 0.01 | 0.04 | 0.01 | 0.02 | 0.05 | 0.03 | 0.05 | 0.04 | 0.01 | 0.03 | 0.03 | 0.06 | 0.01 | 0.02 | 0.06 | 0.02 | 0.00 | 0.18 | 0.07 | 0.01 | 0.00 | 0.04 | 0.00 | 0.00 | 0.13 | 0.03 | 0.15 | 0.20 | 0.01 | 0.02 | 0.05 | 0.05 | 0.05 | 0.11 | 0.20 | 0.02 | 0.05 | 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 |
| MC2R | ENSG00000185231 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.05 | 0.02 | 0.00 | 0.00 | 0.00 | 0.03 | 0.03 | 0.01 | 0.04 | 0.02 | 0.03 | 0.02 | 0.09 | 0.04 | 0.06 | 0.02 | 0.01 | 0.01 | 0.02 | 0.00 | 0.00 | 0.01 | 0.02 | 0.00 | 0.00 | 0.05 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.01 | 0.06 | 0.06 | 0.01 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.10 | 0.02 | 0.02 | 0.00 | 0.00 | 0.02 | 0.08 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 |
| SCNN1B | ENSG00000168447 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.14 | 0.03 | 0.00 | 0.00 | 0.00 | 0.06 | 0.04 | 0.01 | 0.03 | 0.01 | 0.02 | 0.02 | 0.02 | 0.01 | 0.02 | 0.01 | 0.02 | 0.01 | 0.02 | 0.00 | 0.00 | 0.00 | 0.04 | 0.01 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.04 | 0.01 | 0.09 | 0.06 | 0.01 | 0.01 | 0.03 | 0.01 | 0.22 | 0.03 | 0.01 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.09 | 0.00 | 0.00 | 0.02 | 0.00 | 0.06 | 0.00 | 0.00 | 0.01 | 0.03 |
| SLC7A14 | ENSG00000013293 | 0.07 | 0.01 | 0.03 | 0.00 | 0.00 | 0.00 | 0.09 | 0.01 | 0.18 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.23 | 0.01 | 1.75 | 0.00 | 0.61 | 0.00 | 0.92 | 0.00 | 0.31 | 0.00 | 0.03 | 0.01 | 0.04 | 0.01 | 0.09 | 0.00 | 0.15 | 0.01 | 0.12 | 0.03 | 0.10 | 0.00 | 0.00 | 0.07 | 0.00 | 0.00 | 0.25 | 0.01 | 1.43 | 0.02 | 0.76 | 0.00 | 0.40 | 0.00 | 1.14 | 0.06 | 0.07 | 0.07 | 0.19 | 0.00 | 0.00 | 0.00 | 0.06 | 0.00 | 0.04 | 0.01 | 0.05 | 0.02 | 0.00 | 0.00 | 0.03 | 0.03 |
| COL4A5 | ENSG00000188153 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.06 | 0.03 | 0.00 | 0.00 | 0.04 | 0.03 | 0.01 | 0.11 | 0.14 | 0.04 | 0.02 | 0.11 | 0.03 | 0.05 | 0.01 | 0.02 | 0.01 | 0.02 | 0.02 | 0.01 | 0.01 | 0.03 | 0.01 | 0.00 | 0.01 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.03 | 0.09 | 0.06 | 0.07 | 0.03 | 0.02 | 0.02 | 0.04 | 0.02 | 0.08 | 0.17 | 0.00 | 0.01 | 0.00 | 0.00 | 0.04 | 0.02 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.01 |
| ADAMTS7 | ENSG00000136378 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.02 | 0.00 | 0.02 | 0.03 | 0.04 | 0.00 | 0.00 | 0.08 | 0.00 | 0.03 | 0.01 | 0.09 | 0.01 | 0.03 | 0.03 | 0.07 | 0.03 | 0.06 | 0.03 | 0.03 | 0.01 | 0.03 | 0.00 | 0.04 | 0.01 | 0.04 | 0.03 | 0.05 | 0.01 | 0.06 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.10 | 0.02 | 0.19 | 0.12 | 0.13 | 0.01 | 0.03 | 0.03 | 0.13 | 0.05 | 0.06 | 0.05 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.00 | 0.01 | 0.01 | 0.01 | 0.02 | 0.00 | 0.00 | 0.15 | 0.01 |
| SMOX | ENSG00000088826 | 0.01 | 0.00 | 0.01 | 0.00 | 0.05 | 0.00 | 0.01 | 0.03 | 0.03 | 0.03 | 0.00 | 0.00 | 0.00 | 0.05 | 0.03 | 0.04 | 0.12 | 0.01 | 0.03 | 0.03 | 0.07 | 0.03 | 0.05 | 0.01 | 0.06 | 0.04 | 0.05 | 0.08 | 0.00 | 0.03 | 0.04 | 0.02 | 0.00 | 0.03 | 0.05 | 0.08 | 0.00 | 0.01 | 0.00 | 0.00 | 0.06 | 0.05 | 0.29 | 0.08 | 0.05 | 0.01 | 0.09 | 0.03 | 0.09 | 0.06 | 0.07 | 0.09 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.01 | 0.01 | 0.02 | 0.00 | 0.03 | 0.02 |
| CASQ2 | ENSG00000118729 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.04 | 0.09 | 0.05 | 0.00 | 0.00 | 0.00 | 0.30 | 0.02 | 0.14 | 0.02 | 0.17 | 0.00 | 0.16 | 0.16 | 0.16 | 0.02 | 0.08 | 0.00 | 0.07 | 0.01 | 0.07 | 0.12 | 0.02 | 0.01 | 0.03 | 0.00 | 0.10 | 0.05 | 0.05 | 0.03 | 0.26 | 0.00 | 0.00 | 0.05 | 0.08 | 0.17 | 0.13 | 0.01 | 0.08 | 0.04 | 0.03 | 0.08 | 0.06 | 0.05 | 0.11 | 0.04 | 0.03 | 0.00 | 0.01 | 0.03 | 0.09 | 0.00 | 0.01 | 0.01 | 0.03 | 0.00 | 0.03 | 0.09 | 0.09 |
| NFATC1 | ENSG00000131196 | 0.00 | 0.02 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.11 | 0.02 | 0.13 | 0.00 | 0.00 | 0.01 | 0.04 | 0.03 | 0.10 | 0.04 | 0.14 | 0.01 | 0.20 | 0.04 | 0.19 | 0.05 | 0.17 | 0.01 | 0.10 | 0.01 | 0.14 | 0.00 | 0.05 | 0.04 | 0.07 | 0.00 | 0.18 | 0.04 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.09 | 0.09 | 0.44 | 0.03 | 0.06 | 0.04 | 0.10 | 0.12 | 0.12 | 0.16 | 0.14 | 0.00 | 0.10 | 0.00 | 0.02 | 0.08 | 0.05 | 0.01 | 0.06 | 0.02 | 0.05 | 0.00 | 0.04 | 0.02 | 0.03 |
| SLAMF7 | ENSG00000026751 | 0.03 | 0.00 | 0.01 | 0.01 | 0.00 | 0.03 | 0.02 | 0.04 | 0.87 | 0.00 | 0.02 | 0.00 | 0.10 | 0.02 | 0.27 | 0.00 | 0.29 | 0.00 | 0.06 | 0.00 | 0.29 | 0.00 | 0.14 | 0.00 | 0.03 | 0.00 | 0.11 | 0.00 | 0.07 | 0.00 | 0.30 | 0.00 | 0.30 | 0.01 | 0.16 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.31 | 0.00 | 0.38 | 0.02 | 0.16 | 0.00 | 0.14 | 0.00 | 0.37 | 0.00 | 0.45 | 0.02 | 0.10 | 0.00 | 0.00 | 0.00 | 0.25 | 0.00 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.17 | 0.01 |
| SERPINC1 | ENSG00000117601 | 0.03 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.04 | 0.33 | 0.01 | 0.02 | 0.00 | 0.09 | 0.03 | 0.13 | 0.00 | 0.21 | 0.01 | 0.04 | 0.00 | 0.21 | 0.02 | 0.11 | 0.01 | 0.04 | 0.00 | 0.12 | 0.00 | 0.05 | 0.00 | 0.23 | 0.00 | 0.17 | 0.01 | 0.00 | 0.04 | 0.04 | 0.00 | 0.00 | 0.00 | 0.17 | 0.01 | 0.34 | 0.03 | 0.12 | 0.00 | 0.11 | 0.00 | 0.31 | 0.00 | 0.36 | 0.03 | 0.10 | 0.00 | 0.00 | 0.00 | 0.30 | 0.00 | 0.01 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.14 | 0.01 |
| ELN | ENSG00000049540 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.03 | 0.02 | 0.00 | 0.00 | 0.02 | 0.00 | 0.02 | 0.02 | 0.07 | 0.02 | 0.04 | 0.03 | 0.21 | 0.03 | 0.09 | 0.02 | 0.01 | 0.01 | 0.01 | 0.00 | 0.02 | 0.00 | 0.05 | 0.01 | 0.00 | 0.01 | 0.15 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.08 | 0.02 | 0.17 | 0.06 | 0.05 | 0.01 | 0.05 | 0.02 | 0.11 | 0.00 | 0.09 | 0.05 | 0.12 | 0.00 | 0.00 | 0.00 | 0.10 | 0.00 | 0.01 | 0.01 | 0.07 | 0.00 | 0.00 | 0.00 | 0.06 | 0.02 |
| MAP4K2 | ENSG00000168067 | 0.01 | 0.00 | 0.00 | 0.01 | 0.07 | 0.00 | 0.03 | 0.01 | 0.11 | 0.01 | 0.00 | 0.00 | 0.08 | 0.00 | 0.06 | 0.03 | 0.07 | 0.02 | 0.18 | 0.02 | 0.14 | 0.04 | 0.03 | 0.03 | 0.01 | 0.01 | 0.04 | 0.03 | 0.00 | 0.02 | 0.01 | 0.03 | 0.00 | 0.07 | 0.08 | 0.03 | 0.01 | 0.01 | 0.00 | 0.00 | 0.08 | 0.08 | 0.17 | 0.04 | 0.11 | 0.01 | 0.09 | 0.02 | 0.22 | 0.06 | 0.09 | 0.02 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.05 | 0.05 |
| PARM1 | ENSG00000169116 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.03 | 0.01 | 0.15 | 0.02 | 0.00 | 0.00 | 0.00 | 0.08 | 0.07 | 0.02 | 0.21 | 0.01 | 0.08 | 0.01 | 0.18 | 0.02 | 0.07 | 0.02 | 0.01 | 0.01 | 0.04 | 0.01 | 0.01 | 0.01 | 0.02 | 0.08 | 0.00 | 0.03 | 0.06 | 0.00 | 0.02 | 0.02 | 0.00 | 0.00 | 0.13 | 0.02 | 0.28 | 0.11 | 0.07 | 0.02 | 0.03 | 0.01 | 0.05 | 0.05 | 0.07 | 0.06 | 0.07 | 0.01 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.02 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.01 |
| TUSC3 | ENSG00000104723 | 0.00 | 0.02 | 0.00 | 0.01 | 0.00 | 0.03 | 0.01 | 0.16 | 0.02 | 0.14 | 0.00 | 0.00 | 0.02 | 0.05 | 0.01 | 0.06 | 0.01 | 0.09 | 0.01 | 0.08 | 0.07 | 0.06 | 0.10 | 0.03 | 0.01 | 0.12 | 0.00 | 0.18 | 0.02 | 0.05 | 0.01 | 0.11 | 0.00 | 0.05 | 0.00 | 0.02 | 0.00 | 0.08 | 0.00 | 0.00 | 0.03 | 0.14 | 0.01 | 0.43 | 0.01 | 0.05 | 0.01 | 0.08 | 0.10 | 0.21 | 0.09 | 0.06 | 0.06 | 0.01 | 0.00 | 0.00 | 0.00 | 0.09 | 0.00 | 0.02 | 0.00 | 0.04 | 0.00 | 0.01 | 0.01 | 0.04 |
| SLC5A10 | ENSG00000154025 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.08 | 0.08 | 0.00 | 0.01 | 0.00 | 0.02 | 0.06 | 0.05 | 0.07 | 0.04 | 0.02 | 0.04 | 0.07 | 0.07 | 0.03 | 0.06 | 0.00 | 0.02 | 0.02 | 0.04 | 0.03 | 0.00 | 0.11 | 0.05 | 0.06 | 0.03 | 0.01 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.08 | 0.06 | 0.01 | 0.16 | 0.01 | 0.04 | 0.06 | 0.06 | 0.07 | 0.23 | 0.71 | 0.03 | 0.01 | 0.00 | 0.00 | 0.01 | 0.06 | 0.00 | 0.00 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.03 | 0.03 |
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