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 |
| BDKRB2 | ENSG00000168398 | 0.00 | 0.02 | 0.01 | 0.01 | 0.00 | 0.04 | 0.01 | 0.04 | 0.05 | 0.06 | 0.00 | 0.00 | 0.00 | 0.05 | 0.03 | 0.06 | 0.15 | 0.02 | 0.06 | 0.04 | 0.07 | 0.05 | 0.04 | 0.05 | 0.00 | 0.03 | 0.01 | 0.02 | 0.01 | 0.02 | 0.01 | 0.11 | 0.00 | 0.31 | 0.15 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.04 | 0.08 | 0.21 | 0.17 | 0.07 | 0.09 | 0.05 | 0.03 | 0.06 | 0.02 | 0.10 | 0.10 | 0.03 | 0.01 | 0.00 | 0.00 | 0.03 | 0.00 | 0.00 | 0.09 | 0.02 | 0.06 | 0.03 | 0.01 | 0.01 | 0.06 |
| MLKL | ENSG00000168404 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.06 | 0.01 | 0.21 | 0.11 | 0.02 | 0.00 | 0.00 | 0.00 | 0.12 | 0.06 | 0.05 | 0.04 | 0.04 | 0.02 | 0.02 | 0.04 | 0.02 | 0.04 | 0.03 | 0.01 | 0.01 | 0.02 | 0.02 | 0.01 | 0.00 | 0.01 | 0.05 | 0.05 | 0.01 | 0.05 | 0.07 | 0.00 | 0.00 | 0.00 | 0.01 | 0.04 | 0.05 | 0.05 | 0.28 | 0.04 | 0.02 | 0.03 | 0.08 | 0.01 | 0.25 | 0.01 | 0.05 | 0.01 | 0.08 | 0.00 | 0.05 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.04 | 0.00 | 0.00 | 0.01 | 0.04 |
| MTNR1A | ENSG00000168412 | 0.00 | 0.03 | 0.01 | 0.02 | 0.10 | 0.04 | 0.02 | 0.03 | 0.03 | 0.20 | 0.00 | 0.02 | 0.00 | 0.09 | 0.02 | 0.12 | 0.03 | 0.21 | 0.03 | 0.19 | 0.07 | 0.16 | 0.02 | 0.21 | 0.01 | 0.12 | 0.02 | 0.10 | 0.00 | 0.05 | 0.06 | 0.20 | 0.00 | 0.35 | 0.19 | 0.18 | 0.01 | 0.07 | 0.00 | 0.00 | 0.06 | 0.13 | 0.08 | 0.41 | 0.06 | 0.20 | 0.03 | 0.09 | 0.09 | 0.23 | 0.05 | 0.33 | 0.02 | 0.00 | 0.00 | 0.00 | 0.03 | 0.12 | 0.00 | 0.12 | 0.00 | 0.09 | 0.00 | 0.00 | 0.05 | 0.10 |
| KCNG4 | ENSG00000168418 | 0.00 | 0.00 | 0.00 | 0.04 | 0.00 | 0.08 | 0.00 | 0.28 | 0.07 | 0.05 | 0.00 | 0.00 | 0.00 | 0.17 | 0.01 | 0.09 | 0.03 | 0.08 | 0.03 | 0.04 | 0.06 | 0.04 | 0.03 | 0.04 | 0.01 | 0.03 | 0.02 | 0.04 | 0.02 | 0.02 | 0.00 | 0.06 | 0.05 | 0.01 | 0.06 | 0.05 | 0.00 | 0.01 | 0.00 | 0.01 | 0.04 | 0.08 | 0.05 | 0.33 | 0.03 | 0.04 | 0.01 | 0.08 | 0.01 | 0.27 | 0.06 | 0.07 | 0.00 | 0.10 | 0.00 | 0.05 | 0.03 | 0.00 | 0.00 | 0.01 | 0.01 | 0.04 | 0.00 | 0.00 | 0.01 | 0.09 |
| KLHL30 | ENSG00000168427 | 0.01 | 0.08 | 0.04 | 0.05 | 0.00 | 0.05 | 0.01 | 0.04 | 0.02 | 0.30 | 0.00 | 0.00 | 0.00 | 0.08 | 0.04 | 0.05 | 0.02 | 0.18 | 0.01 | 0.18 | 0.05 | 0.16 | 0.04 | 0.07 | 0.02 | 0.03 | 0.04 | 0.03 | 0.04 | 0.04 | 0.04 | 0.08 | 0.05 | 0.01 | 0.04 | 0.05 | 0.00 | 0.01 | 0.00 | 0.01 | 0.02 | 0.10 | 0.21 | 0.27 | 0.01 | 0.38 | 0.03 | 0.05 | 0.21 | 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 | 0.01 | 0.15 |
| TXNDC2 | ENSG00000168454 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.05 | 0.03 | 0.00 | 0.00 | 0.00 | 0.02 | 0.04 | 0.01 | 0.02 | 0.02 | 0.01 | 0.02 | 0.06 | 0.05 | 0.06 | 0.01 | 0.03 | 0.03 | 0.01 | 0.02 | 0.02 | 0.00 | 0.01 | 0.00 | 0.03 | 0.05 | 0.01 | 0.06 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.02 | 0.06 | 0.05 | 0.01 | 0.03 | 0.02 | 0.00 | 0.02 | 0.00 | 0.05 | 0.04 | 0.02 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 |
| SFTPC | ENSG00000168484 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.22 | 0.01 | 0.14 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.07 | 0.00 | 0.09 | 0.00 | 0.06 | 0.01 | 0.06 | 0.04 | 0.04 | 0.00 | 0.12 | 0.01 | 0.18 | 0.01 | 0.06 | 0.03 | 0.12 | 0.00 | 0.05 | 0.06 | 0.00 | 0.01 | 0.02 | 0.00 | 0.00 | 0.02 | 0.15 | 0.01 | 0.43 | 0.00 | 0.06 | 0.01 | 0.09 | 0.10 | 0.24 | 0.02 | 0.05 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.11 | 0.00 | 0.01 | 0.01 | 0.02 | 0.00 | 0.01 | 0.01 | 0.04 |
| BMP1 | ENSG00000168487 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.22 | 0.01 | 0.14 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.07 | 0.00 | 0.09 | 0.00 | 0.06 | 0.01 | 0.06 | 0.03 | 0.04 | 0.00 | 0.12 | 0.01 | 0.18 | 0.01 | 0.06 | 0.03 | 0.12 | 0.00 | 0.05 | 0.06 | 0.00 | 0.01 | 0.02 | 0.00 | 0.00 | 0.02 | 0.15 | 0.01 | 0.43 | 0.00 | 0.06 | 0.01 | 0.09 | 0.10 | 0.24 | 0.02 | 0.05 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.11 | 0.00 | 0.01 | 0.01 | 0.02 | 0.00 | 0.01 | 0.01 | 0.04 |
| FEN1 | ENSG00000168496 | 0.01 | 0.00 | 0.00 | 0.01 | 0.09 | 0.00 | 0.01 | 0.01 | 0.11 | 0.01 | 0.00 | 0.00 | 0.14 | 0.00 | 0.06 | 0.01 | 0.05 | 0.02 | 0.11 | 0.02 | 0.13 | 0.02 | 0.03 | 0.03 | 0.01 | 0.02 | 0.02 | 0.02 | 0.00 | 0.02 | 0.07 | 0.03 | 0.16 | 0.07 | 0.08 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.12 | 0.06 | 0.11 | 0.05 | 0.06 | 0.01 | 0.06 | 0.01 | 0.23 | 0.18 | 0.07 | 0.04 | 0.00 | 0.08 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.05 | 0.04 |
| SCGB1D1 | ENSG00000168515 | 0.01 | 0.00 | 0.00 | 0.01 | 0.09 | 0.00 | 0.01 | 0.01 | 0.12 | 0.01 | 0.00 | 0.00 | 0.12 | 0.00 | 0.05 | 0.02 | 0.05 | 0.02 | 0.13 | 0.02 | 0.13 | 0.02 | 0.03 | 0.02 | 0.01 | 0.02 | 0.02 | 0.03 | 0.00 | 0.02 | 0.04 | 0.02 | 0.13 | 0.07 | 0.08 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.10 | 0.06 | 0.16 | 0.04 | 0.06 | 0.00 | 0.08 | 0.01 | 0.27 | 0.12 | 0.07 | 0.03 | 0.00 | 0.07 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.04 | 0.05 |
| ING2 | ENSG00000168556 | 0.00 | 0.03 | 0.00 | 0.01 | 0.10 | 0.04 | 0.03 | 0.03 | 0.03 | 0.17 | 0.00 | 0.02 | 0.00 | 0.07 | 0.01 | 0.13 | 0.03 | 0.19 | 0.04 | 0.13 | 0.06 | 0.13 | 0.02 | 0.23 | 0.01 | 0.14 | 0.02 | 0.12 | 0.00 | 0.06 | 0.06 | 0.22 | 0.00 | 0.35 | 0.19 | 0.18 | 0.00 | 0.05 | 0.00 | 0.00 | 0.05 | 0.11 | 0.06 | 0.38 | 0.04 | 0.11 | 0.04 | 0.08 | 0.09 | 0.16 | 0.04 | 0.32 | 0.02 | 0.00 | 0.00 | 0.00 | 0.03 | 0.12 | 0.00 | 0.10 | 0.00 | 0.09 | 0.00 | 0.00 | 0.04 | 0.09 |
| ADAM29 | ENSG00000168594 | 0.00 | 0.03 | 0.00 | 0.03 | 0.10 | 0.04 | 0.03 | 0.05 | 0.04 | 0.19 | 0.00 | 0.02 | 0.00 | 0.05 | 0.02 | 0.11 | 0.03 | 0.18 | 0.02 | 0.11 | 0.05 | 0.12 | 0.02 | 0.16 | 0.02 | 0.10 | 0.02 | 0.07 | 0.00 | 0.05 | 0.06 | 0.16 | 0.00 | 0.19 | 0.10 | 0.11 | 0.00 | 0.04 | 0.00 | 0.01 | 0.04 | 0.10 | 0.06 | 0.36 | 0.05 | 0.10 | 0.02 | 0.06 | 0.09 | 0.16 | 0.06 | 0.24 | 0.02 | 0.00 | 0.00 | 0.00 | 0.03 | 0.09 | 0.01 | 0.10 | 0.00 | 0.07 | 0.00 | 0.00 | 0.03 | 0.07 |
| SLC16A4 | ENSG00000168679 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.06 | 0.05 | 0.06 | 0.00 | 0.00 | 0.00 | 0.35 | 0.01 | 0.14 | 0.02 | 0.14 | 0.00 | 0.12 | 0.06 | 0.12 | 0.04 | 0.07 | 0.00 | 0.07 | 0.00 | 0.06 | 0.00 | 0.02 | 0.02 | 0.03 | 0.00 | 0.10 | 0.04 | 0.04 | 0.00 | 0.26 | 0.00 | 0.00 | 0.04 | 0.10 | 0.14 | 0.15 | 0.01 | 0.08 | 0.02 | 0.03 | 0.01 | 0.06 | 0.05 | 0.12 | 0.03 | 0.04 | 0.00 | 0.00 | 0.00 | 0.05 | 0.00 | 0.01 | 0.01 | 0.02 | 0.00 | 0.03 | 0.08 | 0.10 |
| IL7R | ENSG00000168685 | 0.00 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.02 | 0.01 | 0.14 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.22 | 0.00 | 0.23 | 0.00 | 0.07 | 0.00 | 0.10 | 0.01 | 0.17 | 0.02 | 0.05 | 0.01 | 0.03 | 0.00 | 0.02 | 0.01 | 0.07 | 0.00 | 0.00 | 0.01 | 0.26 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.07 | 0.02 | 0.23 | 0.02 | 0.05 | 0.00 | 0.08 | 0.01 | 0.22 | 0.03 | 0.24 | 0.02 | 0.00 | 0.02 | 0.00 | 0.00 | 0.02 | 0.05 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.16 | 0.02 |
| WFDC12 | ENSG00000168703 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.21 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.05 | 0.08 | 0.01 | 0.01 | 0.02 | 0.11 | 0.00 | 0.20 | 0.00 | 0.19 | 0.00 | 0.14 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.00 | 0.04 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.13 | 0.02 | 0.25 | 0.05 | 0.04 | 0.05 | 0.11 | 0.01 | 0.39 | 0.00 | 0.11 | 0.03 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.01 |
| IL12A | ENSG00000168811 | 0.04 | 0.01 | 0.01 | 0.01 | 0.02 | 0.00 | 0.05 | 0.01 | 0.14 | 0.01 | 0.00 | 0.00 | 0.00 | 0.06 | 0.12 | 0.01 | 1.02 | 0.01 | 0.48 | 0.00 | 0.67 | 0.01 | 0.18 | 0.00 | 0.02 | 0.00 | 0.05 | 0.01 | 0.03 | 0.00 | 0.09 | 0.01 | 0.03 | 0.01 | 0.10 | 0.00 | 0.00 | 0.06 | 0.00 | 0.00 | 0.14 | 0.01 | 0.80 | 0.02 | 0.50 | 0.01 | 0.19 | 0.01 | 0.21 | 0.02 | 0.04 | 0.06 | 0.12 | 0.00 | 0.00 | 0.00 | 0.04 | 0.00 | 0.01 | 0.02 | 0.03 | 0.03 | 0.00 | 0.00 | 0.01 | 0.02 |
| OR13J1 | ENSG00000168828 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.12 | 0.03 | 0.00 | 0.00 | 0.02 | 0.08 | 0.06 | 0.02 | 0.39 | 0.04 | 0.28 | 0.03 | 0.25 | 0.04 | 0.18 | 0.02 | 0.02 | 0.00 | 0.00 | 0.00 | 0.13 | 0.00 | 0.03 | 0.02 | 0.19 | 0.01 | 0.14 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.08 | 0.02 | 0.12 | 0.06 | 0.02 | 0.01 | 0.05 | 0.01 | 0.02 | 0.11 | 0.13 | 0.05 | 0.03 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.04 | 0.05 | 0.00 | 0.03 | 0.08 | 0.05 |
| HTR1E | ENSG00000168830 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.38 | 0.01 | 0.07 | 0.00 | 0.00 | 0.01 | 0.04 | 0.01 | 0.06 | 0.10 | 0.03 | 0.02 | 0.03 | 0.03 | 0.06 | 0.02 | 0.09 | 0.00 | 0.02 | 0.01 | 0.01 | 0.00 | 0.03 | 0.04 | 0.06 | 0.00 | 0.11 | 0.08 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.11 | 0.15 | 0.12 | 0.02 | 0.01 | 0.03 | 0.02 | 0.10 | 0.06 | 0.04 | 0.12 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.22 | 0.00 | 0.01 | 0.00 | 0.03 | 0.05 | 0.00 | 0.03 | 0.04 |
| USP39 | ENSG00000168883 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.02 | 0.02 | 0.09 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.03 | 0.01 | 0.12 | 0.01 | 0.08 | 0.01 | 0.12 | 0.01 | 0.05 | 0.01 | 0.00 | 0.01 | 0.01 | 0.01 | 0.01 | 0.01 | 0.05 | 0.02 | 0.00 | 0.02 | 0.04 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.05 | 0.02 | 0.14 | 0.04 | 0.07 | 0.00 | 0.09 | 0.01 | 0.19 | 0.03 | 0.26 | 0.03 | 0.03 | 0.04 | 0.00 | 0.00 | 0.04 | 0.04 | 0.00 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 |
| BTNL3 | ENSG00000168903 | 0.33 | 0.00 | 0.06 | 0.01 | 0.00 | 0.04 | 0.03 | 0.01 | 0.02 | 0.10 | 0.00 | 0.01 | 0.03 | 0.05 | 0.09 | 0.03 | 0.04 | 0.06 | 0.04 | 0.06 | 0.18 | 0.02 | 0.03 | 0.05 | 0.03 | 0.01 | 0.04 | 0.04 | 0.03 | 0.01 | 0.14 | 0.05 | 0.05 | 0.01 | 0.38 | 0.03 | 0.01 | 0.03 | 0.01 | 0.00 | 0.10 | 0.05 | 0.23 | 0.15 | 0.04 | 0.04 | 0.07 | 0.03 | 0.21 | 0.02 | 0.23 | 0.11 | 0.00 | 0.01 | 0.00 | 0.02 | 0.02 | 0.00 | 0.01 | 0.06 | 0.03 | 0.04 | 0.04 | 0.02 | 0.08 | 0.07 |
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