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 |
| OR7E5P | ENSG00000214880 | 0.01 | 0.00 | 0.00 | 0.01 | 0.08 | 0.00 | 0.01 | 0.03 | 0.13 | 0.04 | 0.00 | 0.01 | 0.04 | 0.03 | 0.04 | 0.03 | 0.08 | 0.03 | 0.11 | 0.01 | 0.16 | 0.05 | 0.01 | 0.04 | 0.02 | 0.01 | 0.01 | 0.02 | 0.00 | 0.01 | 0.02 | 0.02 | 0.05 | 0.07 | 0.07 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.09 | 0.07 | 0.12 | 0.06 | 0.04 | 0.02 | 0.04 | 0.03 | 0.34 | 0.03 | 0.10 | 0.05 | 0.01 | 0.03 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.02 | 0.01 | 0.02 | 0.00 | 0.02 | 0.05 | 0.04 |
| GPR33 | ENSG00000214943 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.04 | 0.07 | 0.00 | 0.00 | 0.00 | 0.02 | 0.38 | 0.01 | 0.11 | 0.05 | 0.05 | 0.04 | 0.16 | 0.04 | 0.07 | 0.03 | 0.03 | 0.02 | 0.01 | 0.06 | 0.00 | 0.01 | 0.05 | 0.02 | 0.05 | 0.02 | 0.12 | 0.04 | 0.00 | 0.01 | 0.00 | 0.00 | 0.15 | 0.02 | 0.17 | 0.11 | 0.08 | 0.01 | 0.05 | 0.02 | 0.04 | 0.07 | 0.19 | 0.04 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.01 | 0.09 | 0.00 | 0.00 | 0.02 | 0.02 |
| COL28A1 | ENSG00000215018 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.14 | 0.01 | 0.00 | 0.00 | 0.08 | 0.00 | 0.11 | 0.01 | 0.13 | 0.01 | 0.09 | 0.01 | 0.20 | 0.02 | 0.12 | 0.02 | 0.05 | 0.00 | 0.06 | 0.00 | 0.01 | 0.00 | 0.07 | 0.01 | 0.01 | 0.05 | 0.11 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.04 | 0.09 | 0.37 | 0.02 | 0.01 | 0.03 | 0.05 | 0.08 | 0.03 | 0.19 | 0.05 | 0.14 | 0.01 | 0.00 | 0.01 | 0.05 | 0.00 | 0.00 | 0.01 | 0.03 | 0.01 | 0.00 | 0.00 | 0.16 | 0.00 |
| PRSS41 | ENSG00000215148 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.01 | 0.15 | 0.00 | 0.00 | 0.04 | 0.02 | 0.04 | 0.03 | 0.03 | 0.09 | 0.04 | 0.03 | 0.05 | 0.08 | 0.03 | 0.08 | 0.03 | 0.03 | 0.03 | 0.02 | 0.01 | 0.02 | 0.03 | 0.02 | 0.00 | 0.05 | 0.11 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.09 | 0.02 | 0.10 | 0.16 | 0.11 | 0.02 | 0.06 | 0.03 | 0.03 | 0.05 | 0.09 | 0.03 | 0.01 | 0.00 | 0.00 | 0.00 | 0.09 | 0.00 | 0.01 | 0.00 | 0.04 | 0.01 | 0.00 | 0.00 | 0.05 | 0.01 |
| MUC5AC | ENSG00000215182 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |
| MSMP | ENSG00000215183 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.12 | 0.03 | 0.00 | 0.00 | 0.01 | 0.09 | 0.07 | 0.03 | 0.39 | 0.04 | 0.29 | 0.03 | 0.27 | 0.03 | 0.18 | 0.02 | 0.02 | 0.00 | 0.02 | 0.00 | 0.19 | 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 | 0.07 | 0.01 | 0.02 | 0.13 | 0.13 | 0.04 | 0.03 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.05 | 0.06 | 0.00 | 0.03 | 0.09 | 0.05 |
| KCNU1 | ENSG00000215262 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.07 | 0.31 | 0.05 | 0.00 | 0.00 | 0.02 | 0.03 | 0.10 | 0.04 | 0.53 | 0.06 | 0.21 | 0.04 | 0.37 | 0.08 | 0.08 | 0.03 | 0.12 | 0.04 | 0.07 | 0.04 | 0.06 | 0.02 | 0.04 | 0.07 | 0.00 | 0.09 | 0.05 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.55 | 0.06 | 0.16 | 0.12 | 0.05 | 0.04 | 0.10 | 0.06 | 0.49 | 0.14 | 0.16 | 0.06 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.02 | 0.00 | 0.01 | 0.02 | 0.03 |
| DDX3X | ENSG00000215301 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.04 | 0.02 | 0.00 | 0.00 | 0.00 | 0.05 | 0.05 | 0.02 | 0.02 | 0.04 | 0.00 | 0.04 | 0.05 | 0.06 | 0.02 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.06 | 0.00 | 0.00 | 0.01 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.02 | 0.09 | 0.11 | 0.00 | 0.03 | 0.01 | 0.02 | 0.13 | 0.06 | 0.14 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.06 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 |
| DEFB116 | ENSG00000215545 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.01 | 0.00 | 0.28 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.13 | 0.01 | 0.28 | 0.01 | 0.17 | 0.00 | 0.09 | 0.00 | 0.07 | 0.01 | 0.17 | 0.00 | 0.21 | 0.00 | 0.02 | 0.01 | 0.03 | 0.00 | 0.00 | 0.01 | 0.03 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.06 | 0.01 | 0.27 | 0.02 | 0.26 | 0.00 | 0.11 | 0.00 | 0.94 | 0.00 | 0.15 | 0.02 | 0.23 | 0.00 | 0.05 | 0.00 | 0.08 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 |
| DEFB115 | ENSG00000215547 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.02 | 0.00 | 0.27 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.12 | 0.02 | 0.27 | 0.01 | 0.16 | 0.01 | 0.09 | 0.00 | 0.07 | 0.00 | 0.17 | 0.01 | 0.20 | 0.00 | 0.02 | 0.01 | 0.03 | 0.00 | 0.00 | 0.01 | 0.04 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.06 | 0.01 | 0.27 | 0.02 | 0.24 | 0.01 | 0.11 | 0.00 | 0.94 | 0.01 | 0.13 | 0.03 | 0.23 | 0.00 | 0.05 | 0.00 | 0.08 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 |
| GCGR | ENSG00000215644 | 0.02 | 0.00 | 0.05 | 0.00 | 0.02 | 0.00 | 0.03 | 0.02 | 0.22 | 0.00 | 0.00 | 0.00 | 0.12 | 0.02 | 0.18 | 0.02 | 0.19 | 0.06 | 0.07 | 0.06 | 0.12 | 0.09 | 0.11 | 0.04 | 0.05 | 0.00 | 0.05 | 0.02 | 0.02 | 0.09 | 0.31 | 0.01 | 0.15 | 0.01 | 0.18 | 0.00 | 0.04 | 0.01 | 0.00 | 0.00 | 0.33 | 0.05 | 0.41 | 0.06 | 0.10 | 0.09 | 0.19 | 0.01 | 0.67 | 0.07 | 0.17 | 0.11 | 0.06 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.01 | 0.04 | 0.01 | 0.14 | 0.00 | 0.24 | 0.03 |
| TNFRSF25 | ENSG00000215788 | 0.00 | 0.06 | 0.01 | 0.09 | 0.00 | 0.00 | 0.01 | 0.05 | 0.10 | 0.09 | 0.00 | 0.02 | 0.04 | 0.31 | 0.07 | 0.05 | 0.09 | 0.11 | 0.06 | 0.08 | 0.19 | 0.08 | 0.10 | 0.09 | 0.01 | 0.14 | 0.00 | 0.20 | 0.04 | 0.06 | 0.03 | 0.31 | 0.00 | 1.09 | 0.03 | 0.23 | 0.01 | 0.11 | 0.00 | 0.00 | 0.03 | 0.19 | 0.27 | 0.35 | 0.06 | 0.10 | 0.06 | 0.11 | 0.09 | 0.26 | 0.17 | 0.24 | 0.08 | 0.12 | 0.02 | 0.01 | 0.00 | 0.15 | 0.00 | 0.06 | 0.02 | 0.28 | 0.00 | 0.05 | 0.06 | 0.14 |
| SLC35E2 | ENSG00000215790 | 0.00 | 0.05 | 0.01 | 0.10 | 0.00 | 0.00 | 0.02 | 0.03 | 0.10 | 0.08 | 0.00 | 0.02 | 0.04 | 0.27 | 0.09 | 0.06 | 0.08 | 0.11 | 0.06 | 0.09 | 0.13 | 0.08 | 0.09 | 0.09 | 0.02 | 0.11 | 0.00 | 0.17 | 0.05 | 0.05 | 0.02 | 0.31 | 0.00 | 1.01 | 0.05 | 0.17 | 0.01 | 0.12 | 0.00 | 0.00 | 0.04 | 0.19 | 0.23 | 0.38 | 0.06 | 0.11 | 0.05 | 0.12 | 0.08 | 0.27 | 0.18 | 0.28 | 0.10 | 0.12 | 0.02 | 0.00 | 0.00 | 0.19 | 0.00 | 0.03 | 0.03 | 0.15 | 0.00 | 0.14 | 0.07 | 0.13 |
| RPTN | ENSG00000215853 | 0.04 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.06 | 0.01 | 0.51 | 0.01 | 0.02 | 0.00 | 0.11 | 0.02 | 0.41 | 0.00 | 0.30 | 0.00 | 0.06 | 0.01 | 0.29 | 0.00 | 0.21 | 0.00 | 0.02 | 0.00 | 0.17 | 0.01 | 0.07 | 0.00 | 0.35 | 0.00 | 0.43 | 0.01 | 0.22 | 0.00 | 0.10 | 0.00 | 0.00 | 0.00 | 0.34 | 0.00 | 0.59 | 0.02 | 0.23 | 0.00 | 0.22 | 0.00 | 0.58 | 0.00 | 0.51 | 0.01 | 0.12 | 0.01 | 0.00 | 0.00 | 0.24 | 0.04 | 0.01 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.21 | 0.01 |
| MMP23A | ENSG00000215914 | 0.00 | 0.05 | 0.01 | 0.10 | 0.00 | 0.00 | 0.02 | 0.03 | 0.10 | 0.08 | 0.00 | 0.02 | 0.04 | 0.27 | 0.09 | 0.06 | 0.08 | 0.11 | 0.06 | 0.09 | 0.13 | 0.08 | 0.09 | 0.09 | 0.02 | 0.11 | 0.00 | 0.17 | 0.05 | 0.05 | 0.02 | 0.31 | 0.00 | 1.01 | 0.05 | 0.17 | 0.01 | 0.12 | 0.00 | 0.00 | 0.04 | 0.19 | 0.23 | 0.38 | 0.06 | 0.11 | 0.05 | 0.12 | 0.08 | 0.27 | 0.18 | 0.28 | 0.10 | 0.12 | 0.02 | 0.00 | 0.00 | 0.19 | 0.00 | 0.03 | 0.03 | 0.15 | 0.00 | 0.14 | 0.07 | 0.13 |
| IFI30 | ENSG00000216490 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.03 | 0.00 | 0.03 | 0.05 | 0.01 | 0.03 | 0.02 | 0.09 | 0.02 | 0.05 | 0.02 | 0.11 | 0.01 | 0.04 | 0.02 | 0.01 | 0.00 | 0.01 | 0.04 | 0.01 | 0.02 | 0.09 | 0.03 | 0.06 | 0.03 | 0.13 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.08 | 0.02 | 0.52 | 0.04 | 0.02 | 0.02 | 0.18 | 0.03 | 0.33 | 0.07 | 0.07 | 0.02 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.01 | 0.01 | 0.02 | 0.00 | 0.03 | 0.01 |
| CKLF | ENSG00000217555 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.06 | 0.00 | 0.06 | 0.11 | 0.02 | 0.00 | 0.00 | 0.00 | 0.06 | 0.05 | 0.03 | 0.04 | 0.01 | 0.03 | 0.01 | 0.11 | 0.00 | 0.03 | 0.02 | 0.01 | 0.00 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.04 | 0.05 | 0.01 | 0.23 | 0.03 | 0.01 | 0.02 | 0.00 | 0.01 | 0.02 | 0.05 | 0.04 | 0.28 | 0.02 | 0.04 | 0.03 | 0.07 | 0.05 | 0.14 | 0.02 | 0.06 | 0.15 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.03 | 0.03 | 0.01 |
| TDRD15 | ENSG00000218819 | 0.00 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 | 0.10 | 0.01 | 0.00 | 0.00 | 0.03 | 0.05 | 0.05 | 0.02 | 0.10 | 0.03 | 0.03 | 0.02 | 0.06 | 0.04 | 0.02 | 0.04 | 0.01 | 0.01 | 0.00 | 0.02 | 0.01 | 0.04 | 0.10 | 0.01 | 0.00 | 0.05 | 0.01 | 0.04 | 0.01 | 0.00 | 0.00 | 0.00 | 0.04 | 0.04 | 0.20 | 0.14 | 0.09 | 0.00 | 0.10 | 0.03 | 0.19 | 0.03 | 0.03 | 0.10 | 0.18 | 0.01 | 0.00 | 0.00 | 0.00 | 0.07 | 0.01 | 0.01 | 0.02 | 0.02 | 0.05 | 0.00 | 0.01 | 0.04 |
| FAM19A5 | ENSG00000219438 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.03 | 0.01 | 0.03 | 0.01 | 0.13 | 0.00 | 0.03 | 0.00 | 0.06 | 0.02 | 0.12 | 0.06 | 0.08 | 0.02 | 0.04 | 0.03 | 0.04 | 0.03 | 0.07 | 0.01 | 0.06 | 0.01 | 0.11 | 0.01 | 0.09 | 0.07 | 0.07 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.06 | 0.00 | 0.02 | 0.06 | 0.07 | 0.02 | 0.64 | 0.03 | 0.09 | 0.04 | 0.15 | 0.06 | 0.29 | 0.07 | 0.16 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.09 | 0.00 | 0.05 | 0.00 | 0.11 | 0.00 | 0.00 | 0.14 | 0.05 |
| VAMP2 | ENSG00000220205 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.16 | 0.03 | 0.03 | 0.00 | 0.01 | 0.00 | 0.03 | 0.01 | 0.05 | 0.01 | 0.02 | 0.02 | 0.03 | 0.03 | 0.04 | 0.01 | 0.03 | 0.00 | 0.02 | 0.00 | 0.02 | 0.01 | 0.02 | 0.00 | 0.16 | 0.00 | 0.08 | 0.01 | 0.05 | 0.01 | 0.03 | 0.00 | 0.00 | 0.01 | 0.06 | 0.07 | 0.07 | 0.00 | 0.05 | 0.04 | 0.05 | 0.06 | 0.15 | 0.19 | 0.28 | 0.00 | 0.02 | 0.02 | 0.01 | 0.00 | 0.10 | 0.01 | 0.00 | 0.00 | 0.06 | 0.00 | 0.00 | 0.00 | 0.04 |
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