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 |
| FBXL19 | ENSG00000099364 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.09 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.11 | 0.01 | 0.10 | 0.01 | 0.03 | 0.02 | 0.10 | 0.00 | 0.07 | 0.00 | 0.07 | 0.00 | 0.10 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.10 | 0.01 | 0.10 | 0.03 | 0.02 | 0.03 | 0.15 | 0.00 | 0.62 | 0.05 | 0.06 | 0.02 | 0.02 | 0.01 | 0.00 | 0.02 | 0.05 | 0.02 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 |
| BMPR1A | ENSG00000107779 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.18 | 0.06 | 0.08 | 0.00 | 0.02 | 0.01 | 0.12 | 0.01 | 0.03 | 0.03 | 0.09 | 0.01 | 0.07 | 0.03 | 0.12 | 0.04 | 0.12 | 0.01 | 0.09 | 0.00 | 0.07 | 0.01 | 0.02 | 0.03 | 0.05 | 0.25 | 0.02 | 0.03 | 0.01 | 0.00 | 0.01 | 0.00 | 0.01 | 0.03 | 0.07 | 0.09 | 0.27 | 0.02 | 0.07 | 0.09 | 0.07 | 0.02 | 0.12 | 0.01 | 0.08 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.06 | 0.01 | 0.03 | 0.02 | 0.05 | 0.00 | 0.00 | 0.00 | 0.03 |
| PDE3A | ENSG00000172572 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.02 | 0.07 | 0.05 | 0.03 | 0.01 | 0.00 | 0.02 | 0.04 | 0.15 | 0.05 | 0.13 | 0.01 | 0.08 | 0.02 | 0.11 | 0.03 | 0.11 | 0.03 | 0.02 | 0.02 | 0.11 | 0.03 | 0.07 | 0.06 | 0.01 | 0.03 | 0.14 | 0.08 | 0.03 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.08 | 0.05 | 0.31 | 0.08 | 0.01 | 0.01 | 0.05 | 0.01 | 0.15 | 0.03 | 0.16 | 0.13 | 0.59 | 0.00 | 0.01 | 0.01 | 0.00 | 0.04 | 0.07 | 0.01 | 0.03 | 0.04 | 0.00 | 0.00 | 0.06 | 0.01 |
| A2M | ENSG00000175899 | 0.01 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.10 | 0.07 | 0.03 | 0.01 | 0.00 | 0.00 | 0.05 | 0.05 | 0.08 | 0.12 | 0.01 | 0.11 | 0.03 | 0.08 | 0.02 | 0.07 | 0.08 | 0.02 | 0.02 | 0.04 | 0.03 | 0.01 | 0.07 | 0.04 | 0.05 | 0.14 | 0.05 | 0.03 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.09 | 0.05 | 0.31 | 0.10 | 0.03 | 0.03 | 0.03 | 0.03 | 0.00 | 0.03 | 0.11 | 0.11 | 0.55 | 0.00 | 0.00 | 0.01 | 0.00 | 0.08 | 0.11 | 0.01 | 0.03 | 0.04 | 0.00 | 0.01 | 0.05 | 0.04 |
| BMP2 | ENSG00000125845 | 0.01 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.02 | 0.02 | 0.04 | 0.02 | 0.00 | 0.00 | 0.00 | 0.05 | 0.03 | 0.04 | 0.13 | 0.01 | 0.05 | 0.02 | 0.07 | 0.02 | 0.04 | 0.01 | 0.03 | 0.04 | 0.06 | 0.07 | 0.00 | 0.02 | 0.04 | 0.00 | 0.00 | 0.01 | 0.03 | 0.08 | 0.00 | 0.01 | 0.00 | 0.00 | 0.05 | 0.04 | 0.25 | 0.07 | 0.06 | 0.01 | 0.05 | 0.02 | 0.03 | 0.06 | 0.09 | 0.04 | 0.00 | 0.02 | 0.00 | 0.00 | 0.06 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.02 | 0.00 | 0.02 | 0.02 |
| CETP | ENSG00000087237 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.05 | 0.01 | 0.05 | 0.00 | 0.03 | 0.00 | 0.01 | 0.05 | 0.03 | 0.04 | 0.03 | 0.03 | 0.03 | 0.10 | 0.01 | 0.01 | 0.04 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.01 | 0.02 | 0.00 | 0.01 | 0.10 | 0.05 | 0.00 | 0.02 | 0.00 | 0.00 | 0.04 | 0.04 | 0.06 | 0.12 | 0.00 | 0.08 | 0.06 | 0.06 | 0.05 | 0.12 | 0.04 | 0.06 | 0.12 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.01 | 0.01 | 0.02 | 0.00 | 0.03 | 0.00 | 0.04 |
| SLC16A12 | ENSG00000152779 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.20 | 0.03 | 0.12 | 0.00 | 0.02 | 0.01 | 0.12 | 0.01 | 0.04 | 0.02 | 0.10 | 0.01 | 0.07 | 0.02 | 0.13 | 0.00 | 0.10 | 0.00 | 0.09 | 0.00 | 0.08 | 0.01 | 0.02 | 0.04 | 0.06 | 0.20 | 0.07 | 0.00 | 0.01 | 0.01 | 0.01 | 0.00 | 0.02 | 0.01 | 0.10 | 0.08 | 0.30 | 0.01 | 0.10 | 0.05 | 0.10 | 0.09 | 0.12 | 0.01 | 0.10 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.20 | 0.00 | 0.04 | 0.00 | 0.09 | 0.00 | 0.00 | 0.00 | 0.04 |
| MBTPS1 | ENSG00000140943 | 0.00 | 0.00 | 0.00 | 0.04 | 0.00 | 0.08 | 0.00 | 0.26 | 0.09 | 0.04 | 0.00 | 0.00 | 0.01 | 0.17 | 0.01 | 0.09 | 0.04 | 0.08 | 0.03 | 0.04 | 0.06 | 0.04 | 0.03 | 0.04 | 0.01 | 0.03 | 0.02 | 0.04 | 0.01 | 0.01 | 0.00 | 0.06 | 0.05 | 0.01 | 0.06 | 0.07 | 0.00 | 0.01 | 0.00 | 0.01 | 0.04 | 0.08 | 0.05 | 0.32 | 0.03 | 0.04 | 0.01 | 0.08 | 0.01 | 0.24 | 0.05 | 0.08 | 0.00 | 0.12 | 0.00 | 0.04 | 0.03 | 0.00 | 0.00 | 0.01 | 0.01 | 0.04 | 0.00 | 0.00 | 0.01 | 0.09 |
| SECTM1 | ENSG00000141574 | 0.02 | 0.00 | 0.05 | 0.00 | 0.02 | 0.00 | 0.05 | 0.01 | 0.20 | 0.01 | 0.00 | 0.00 | 0.12 | 0.02 | 0.16 | 0.02 | 0.18 | 0.09 | 0.06 | 0.07 | 0.10 | 0.11 | 0.10 | 0.04 | 0.04 | 0.00 | 0.04 | 0.03 | 0.03 | 0.09 | 0.32 | 0.01 | 0.15 | 0.01 | 0.24 | 0.00 | 0.03 | 0.01 | 0.00 | 0.00 | 0.34 | 0.05 | 0.43 | 0.08 | 0.08 | 0.10 | 0.16 | 0.02 | 0.51 | 0.08 | 0.21 | 0.16 | 0.06 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.07 | 0.02 | 0.03 | 0.02 | 0.14 | 0.00 | 0.24 | 0.03 |
| CDK12 | ENSG00000167258 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.03 | 0.23 | 0.01 | 0.00 | 0.01 | 0.01 | 0.04 | 0.16 | 0.01 | 0.15 | 0.04 | 0.15 | 0.01 | 0.94 | 0.02 | 0.74 | 0.01 | 0.20 | 0.01 | 0.22 | 0.02 | 0.10 | 0.02 | 0.02 | 0.05 | 0.02 | 0.01 | 0.03 | 0.17 | 0.00 | 0.12 | 0.00 | 0.00 | 0.86 | 0.07 | 0.13 | 0.16 | 0.17 | 0.02 | 0.35 | 0.06 | 0.56 | 0.07 | 0.05 | 0.14 | 0.01 | 0.01 | 0.01 | 0.02 | 0.04 | 0.00 | 0.00 | 0.01 | 0.01 | 0.04 | 0.00 | 0.05 | 0.02 | 0.03 |
| COL27A1 | ENSG00000196739 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.04 | 0.01 | 0.02 | 0.03 | 0.00 | 0.00 | 0.02 | 0.00 | 0.05 | 0.02 | 0.04 | 0.01 | 0.05 | 0.00 | 0.13 | 0.01 | 0.06 | 0.02 | 0.00 | 0.01 | 0.04 | 0.02 | 0.01 | 0.02 | 0.04 | 0.06 | 0.06 | 0.04 | 0.08 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.04 | 0.11 | 0.11 | 0.04 | 0.00 | 0.01 | 0.04 | 0.03 | 0.15 | 0.10 | 0.04 | 0.03 | 0.01 | 0.00 | 0.00 | 0.05 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 |
| TDP1 | ENSG00000042088 | 0.00 | 0.02 | 0.01 | 0.01 | 0.00 | 0.04 | 0.02 | 0.04 | 0.06 | 0.06 | 0.00 | 0.00 | 0.00 | 0.05 | 0.07 | 0.05 | 0.11 | 0.02 | 0.04 | 0.05 | 0.08 | 0.07 | 0.02 | 0.04 | 0.00 | 0.03 | 0.01 | 0.02 | 0.01 | 0.01 | 0.01 | 0.10 | 0.00 | 0.40 | 0.05 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.04 | 0.09 | 0.19 | 0.17 | 0.06 | 0.07 | 0.04 | 0.01 | 0.08 | 0.05 | 0.05 | 0.10 | 0.03 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.11 | 0.02 | 0.06 | 0.03 | 0.01 | 0.01 | 0.06 |
| ACVR1 | ENSG00000115170 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.09 | 0.07 | 0.04 | 0.00 | 0.01 | 0.00 | 0.00 | 0.05 | 0.01 | 0.09 | 0.03 | 0.05 | 0.02 | 0.09 | 0.03 | 0.06 | 0.04 | 0.00 | 0.01 | 0.00 | 0.02 | 0.05 | 0.02 | 0.04 | 0.07 | 0.00 | 0.05 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.04 | 0.30 | 0.05 | 0.05 | 0.02 | 0.04 | 0.01 | 0.01 | 0.00 | 0.06 | 0.08 | 0.03 | 0.01 | 0.00 | 0.00 | 0.00 | 0.15 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.01 |
| DAPK2 | ENSG00000035664 | 0.00 | 0.00 | 0.00 | 0.01 | 0.17 | 0.00 | 0.01 | 0.02 | 0.02 | 0.04 | 0.00 | 0.00 | 0.08 | 0.00 | 0.04 | 0.04 | 0.05 | 0.02 | 0.02 | 0.02 | 0.03 | 0.04 | 0.03 | 0.04 | 0.02 | 0.03 | 0.03 | 0.02 | 0.02 | 0.01 | 0.04 | 0.01 | 0.00 | 0.01 | 0.09 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.05 | 0.11 | 0.11 | 0.05 | 0.01 | 0.02 | 0.05 | 0.04 | 0.21 | 0.11 | 0.02 | 0.01 | 0.02 | 0.00 | 0.00 | 0.06 | 0.00 | 0.01 | 0.01 | 0.01 | 0.03 | 0.00 | 0.00 | 0.03 | 0.02 |
| BCHE | ENSG00000114200 | 0.05 | 0.00 | 0.03 | 0.01 | 0.00 | 0.00 | 0.07 | 0.02 | 0.16 | 0.01 | 0.00 | 0.00 | 0.00 | 0.04 | 0.15 | 0.01 | 1.41 | 0.00 | 0.54 | 0.00 | 0.77 | 0.00 | 0.21 | 0.01 | 0.03 | 0.01 | 0.04 | 0.00 | 0.03 | 0.00 | 0.09 | 0.01 | 0.08 | 0.01 | 0.10 | 0.00 | 0.00 | 0.06 | 0.00 | 0.00 | 0.19 | 0.01 | 1.05 | 0.02 | 0.63 | 0.01 | 0.24 | 0.01 | 0.35 | 0.00 | 0.08 | 0.09 | 0.18 | 0.00 | 0.00 | 0.00 | 0.04 | 0.00 | 0.02 | 0.01 | 0.04 | 0.03 | 0.00 | 0.00 | 0.02 | 0.03 |
| KCNN4 | ENSG00000104783 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.02 | 0.00 | 0.04 | 0.14 | 0.02 | 0.00 | 0.00 | 0.08 | 0.07 | 0.11 | 0.05 | 0.12 | 0.08 | 0.03 | 0.02 | 0.09 | 0.05 | 0.07 | 0.02 | 0.02 | 0.02 | 0.01 | 0.02 | 0.09 | 0.02 | 0.04 | 0.03 | 0.12 | 0.01 | 0.17 | 0.03 | 0.00 | 0.03 | 0.00 | 0.00 | 0.06 | 0.05 | 0.19 | 0.29 | 0.17 | 0.04 | 0.05 | 0.04 | 0.09 | 0.17 | 0.10 | 0.13 | 0.00 | 0.04 | 0.01 | 0.00 | 0.07 | 0.06 | 0.01 | 0.12 | 0.03 | 0.09 | 0.00 | 0.00 | 0.02 | 0.03 |
| EPOR | ENSG00000187266 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.07 | 0.05 | 0.00 | 0.01 | 0.09 | 0.01 | 0.01 | 0.05 | 0.06 | 0.06 | 0.05 | 0.04 | 0.07 | 0.05 | 0.06 | 0.03 | 0.02 | 0.01 | 0.02 | 0.02 | 0.01 | 0.03 | 0.03 | 0.09 | 0.00 | 0.01 | 0.12 | 0.03 | 0.00 | 0.00 | 0.00 | 0.01 | 0.07 | 0.05 | 0.58 | 0.18 | 0.10 | 0.04 | 0.23 | 0.03 | 0.33 | 0.13 | 0.22 | 0.01 | 0.02 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.04 | 0.00 | 0.02 | 0.02 | 0.02 | 0.02 |
| COL18A1 | ENSG00000182871 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.06 | 0.04 | 0.00 | 0.02 | 0.02 | 0.01 | 0.05 | 0.03 | 0.05 | 0.06 | 0.02 | 0.06 | 0.05 | 0.09 | 0.02 | 0.07 | 0.01 | 0.02 | 0.01 | 0.09 | 0.01 | 0.01 | 0.03 | 0.03 | 0.05 | 0.07 | 0.11 | 0.04 | 0.01 | 0.00 | 0.00 | 0.00 | 0.09 | 0.02 | 0.21 | 0.18 | 0.05 | 0.05 | 0.05 | 0.03 | 0.09 | 0.14 | 0.11 | 0.14 | 0.04 | 0.01 | 0.10 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.02 | 0.03 | 0.03 | 0.00 | 0.02 | 0.04 |
| LTF | ENSG00000012223 | 0.00 | 0.19 | 0.00 | 0.02 | 0.08 | 0.00 | 0.00 | 0.03 | 0.07 | 0.10 | 0.00 | 0.04 | 0.00 | 0.52 | 0.00 | 0.06 | 0.01 | 0.08 | 0.00 | 0.05 | 0.01 | 0.08 | 0.02 | 0.10 | 0.00 | 0.03 | 0.03 | 0.06 | 0.00 | 0.04 | 0.02 | 0.04 | 0.00 | 0.24 | 0.01 | 0.02 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.15 | 0.07 | 0.18 | 0.01 | 0.05 | 0.02 | 0.05 | 0.03 | 0.18 | 0.05 | 0.11 | 0.03 | 0.04 | 0.00 | 0.01 | 0.00 | 0.10 | 0.00 | 0.05 | 0.00 | 0.04 | 0.00 | 0.03 | 0.01 | 0.05 |
| TRPC6 | ENSG00000137672 | 0.02 | 0.01 | 0.00 | 0.05 | 0.03 | 0.03 | 0.02 | 0.05 | 0.26 | 0.06 | 0.00 | 0.00 | 0.06 | 0.08 | 0.10 | 0.04 | 0.10 | 0.07 | 0.40 | 0.09 | 0.17 | 0.08 | 0.07 | 0.04 | 0.04 | 0.01 | 0.02 | 0.02 | 0.04 | 0.01 | 0.04 | 0.06 | 0.00 | 0.10 | 0.00 | 0.05 | 0.00 | 0.04 | 0.00 | 0.00 | 0.06 | 0.17 | 0.32 | 0.11 | 0.91 | 0.09 | 0.06 | 0.04 | 0.07 | 0.17 | 0.20 | 0.15 | 0.02 | 0.07 | 0.02 | 0.00 | 0.04 | 0.01 | 0.02 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.21 | 0.11 |
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