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 |
| OR11H1 | ENSG00000130538 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.00 | 0.01 | 0.02 | 0.10 | 0.05 | 0.00 | 0.00 | 0.00 | 0.05 | 0.16 | 0.04 | 0.20 | 0.07 | 0.09 | 0.06 | 0.11 | 0.07 | 0.07 | 0.04 | 0.03 | 0.02 | 0.01 | 0.09 | 0.01 | 0.04 | 0.08 | 0.00 | 0.00 | 0.02 | 0.13 | 0.03 | 0.01 | 0.02 | 0.00 | 0.00 | 0.10 | 0.03 | 0.40 | 0.12 | 0.07 | 0.02 | 0.08 | 0.03 | 0.21 | 0.08 | 0.17 | 0.09 | 0.02 | 0.01 | 0.00 | 0.01 | 0.01 | 0.00 | 0.02 | 0.03 | 0.01 | 0.09 | 0.00 | 0.00 | 0.03 | 0.03 |
| FIBCD1 | ENSG00000130720 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 | 0.02 | 0.02 | 0.00 | 0.01 | 0.00 | 0.02 | 0.04 | 0.03 | 0.06 | 0.02 | 0.07 | 0.02 | 0.11 | 0.03 | 0.10 | 0.01 | 0.02 | 0.01 | 0.04 | 0.04 | 0.00 | 0.00 | 0.05 | 0.03 | 0.06 | 0.01 | 0.14 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.05 | 0.09 | 0.25 | 0.07 | 0.01 | 0.04 | 0.05 | 0.06 | 0.11 | 0.05 | 0.11 | 0.03 | 0.03 | 0.01 | 0.00 | 0.05 | 0.00 | 0.02 | 0.01 | 0.03 | 0.02 | 0.00 | 0.03 | 0.02 | 0.03 |
| ANGPTL6 | ENSG00000130812 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.01 | 0.09 | 0.04 | 0.00 | 0.01 | 0.09 | 0.01 | 0.03 | 0.04 | 0.07 | 0.06 | 0.05 | 0.05 | 0.08 | 0.06 | 0.03 | 0.05 | 0.02 | 0.01 | 0.01 | 0.04 | 0.01 | 0.03 | 0.02 | 0.11 | 0.00 | 0.01 | 0.10 | 0.03 | 0.01 | 0.00 | 0.00 | 0.01 | 0.10 | 0.04 | 0.55 | 0.20 | 0.11 | 0.06 | 0.17 | 0.10 | 0.56 | 0.21 | 0.31 | 0.03 | 0.02 | 0.00 | 0.03 | 0.00 | 0.00 | 0.03 | 0.01 | 0.00 | 0.05 | 0.00 | 0.02 | 0.02 | 0.02 | 0.01 |
| DUSP9 | ENSG00000130829 | 0.03 | 0.01 | 0.02 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.11 | 0.04 | 0.06 | 0.00 | 0.06 | 0.01 | 0.22 | 0.01 | 0.18 | 0.02 | 0.14 | 0.01 | 0.24 | 0.01 | 0.18 | 0.02 | 0.05 | 0.00 | 0.10 | 0.01 | 0.07 | 0.00 | 0.12 | 0.03 | 0.10 | 0.01 | 0.16 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.10 | 0.03 | 0.44 | 0.09 | 0.22 | 0.02 | 0.11 | 0.03 | 0.17 | 0.07 | 0.24 | 0.07 | 0.01 | 0.02 | 0.00 | 0.00 | 0.15 | 0.07 | 0.02 | 0.03 | 0.03 | 0.01 | 0.05 | 0.00 | 0.06 | 0.01 |
| PKDREJ | ENSG00000130943 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.00 | 0.04 | 0.02 | 0.10 | 0.00 | 0.04 | 0.00 | 0.04 | 0.03 | 0.10 | 0.04 | 0.06 | 0.04 | 0.03 | 0.05 | 0.02 | 0.02 | 0.07 | 0.00 | 0.02 | 0.01 | 0.10 | 0.00 | 0.08 | 0.06 | 0.06 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.06 | 0.00 | 0.00 | 0.04 | 0.06 | 0.03 | 0.52 | 0.04 | 0.07 | 0.04 | 0.12 | 0.06 | 0.27 | 0.05 | 0.13 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.09 | 0.00 | 0.05 | 0.01 | 0.09 | 0.00 | 0.00 | 0.14 | 0.04 |
| HABP4 | ENSG00000130956 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.02 | 0.03 | 0.05 | 0.00 | 0.01 | 0.02 | 0.04 | 0.01 | 0.04 | 0.05 | 0.01 | 0.04 | 0.01 | 0.07 | 0.02 | 0.03 | 0.04 | 0.02 | 0.02 | 0.04 | 0.02 | 0.00 | 0.01 | 0.02 | 0.04 | 0.00 | 0.08 | 0.04 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.04 | 0.04 | 0.16 | 0.02 | 0.02 | 0.01 | 0.04 | 0.00 | 0.15 | 0.11 | 0.02 | 0.03 | 0.02 | 0.00 | 0.02 | 0.00 | 0.02 | 0.00 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.01 | 0.02 |
| SLC35D2 | ENSG00000130958 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.02 | 0.03 | 0.05 | 0.00 | 0.01 | 0.02 | 0.04 | 0.01 | 0.04 | 0.04 | 0.01 | 0.04 | 0.00 | 0.06 | 0.02 | 0.02 | 0.04 | 0.02 | 0.02 | 0.04 | 0.03 | 0.00 | 0.01 | 0.01 | 0.04 | 0.00 | 0.08 | 0.04 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.04 | 0.04 | 0.15 | 0.02 | 0.02 | 0.01 | 0.04 | 0.00 | 0.15 | 0.11 | 0.02 | 0.03 | 0.02 | 0.00 | 0.02 | 0.00 | 0.02 | 0.00 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.01 | 0.02 |
| LILRB2 | ENSG00000131042 | 0.01 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.03 | 0.00 | 0.17 | 0.02 | 0.00 | 0.00 | 0.01 | 0.04 | 0.03 | 0.06 | 0.10 | 0.08 | 0.04 | 0.02 | 0.10 | 0.03 | 0.10 | 0.03 | 0.02 | 0.03 | 0.01 | 0.04 | 0.03 | 0.04 | 0.07 | 0.02 | 0.00 | 0.07 | 0.25 | 0.00 | 0.00 | 0.03 | 0.00 | 0.00 | 0.15 | 0.03 | 0.14 | 0.27 | 0.14 | 0.06 | 0.06 | 0.05 | 0.35 | 0.10 | 0.08 | 0.16 | 0.00 | 0.06 | 0.01 | 0.00 | 0.13 | 0.03 | 0.01 | 0.17 | 0.02 | 0.12 | 0.00 | 0.00 | 0.04 | 0.03 |
| BPIFA2 | ENSG00000131050 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.02 | 0.01 | 0.22 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.07 | 0.02 | 0.21 | 0.00 | 0.19 | 0.00 | 0.09 | 0.00 | 0.05 | 0.01 | 0.11 | 0.00 | 0.17 | 0.00 | 0.01 | 0.01 | 0.02 | 0.00 | 0.00 | 0.01 | 0.05 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.02 | 0.21 | 0.02 | 0.20 | 0.00 | 0.08 | 0.01 | 0.33 | 0.00 | 0.09 | 0.02 | 0.03 | 0.00 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.06 | 0.00 |
| BPIFA3 | ENSG00000131059 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.02 | 0.01 | 0.21 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.07 | 0.01 | 0.22 | 0.00 | 0.19 | 0.00 | 0.09 | 0.00 | 0.05 | 0.01 | 0.11 | 0.00 | 0.17 | 0.00 | 0.02 | 0.01 | 0.02 | 0.00 | 0.00 | 0.01 | 0.05 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.02 | 0.20 | 0.02 | 0.19 | 0.00 | 0.08 | 0.01 | 0.38 | 0.00 | 0.09 | 0.02 | 0.03 | 0.00 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.00 | 0.00 | 0.05 | 0.00 |
| GGT7 | ENSG00000131067 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.01 | 0.02 | 0.15 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.08 | 0.02 | 0.15 | 0.01 | 0.15 | 0.00 | 0.11 | 0.01 | 0.05 | 0.01 | 0.12 | 0.00 | 0.16 | 0.00 | 0.00 | 0.01 | 0.02 | 0.00 | 0.00 | 0.05 | 0.09 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.13 | 0.02 | 0.16 | 0.03 | 0.13 | 0.00 | 0.05 | 0.01 | 0.26 | 0.00 | 0.09 | 0.03 | 0.00 | 0.01 | 0.00 | 0.03 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.01 |
| DEFB118 | ENSG00000131068 | 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 | 0.27 | 0.00 | 0.18 | 0.00 | 0.09 | 0.00 | 0.07 | 0.00 | 0.17 | 0.00 | 0.21 | 0.00 | 0.02 | 0.01 | 0.04 | 0.00 | 0.00 | 0.01 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.07 | 0.01 | 0.29 | 0.02 | 0.27 | 0.00 | 0.12 | 0.00 | 1.04 | 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 |
| PYY | ENSG00000131096 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.16 | 0.04 | 0.03 | 0.01 | 0.01 | 0.02 | 0.04 | 0.08 | 0.01 | 0.04 | 0.06 | 0.02 | 0.02 | 0.11 | 0.01 | 0.10 | 0.03 | 0.02 | 0.01 | 0.03 | 0.03 | 0.05 | 0.01 | 0.04 | 0.03 | 0.08 | 0.01 | 0.07 | 0.14 | 0.00 | 0.09 | 0.00 | 0.00 | 0.03 | 0.10 | 0.03 | 0.14 | 0.04 | 0.03 | 0.04 | 0.07 | 0.08 | 0.19 | 0.05 | 0.06 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.02 | 0.00 | 0.05 | 0.01 | 0.05 |
| CCL25 | ENSG00000131142 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.02 | 0.00 | 0.02 | 0.06 | 0.09 | 0.00 | 0.01 | 0.01 | 0.07 | 0.01 | 0.06 | 0.05 | 0.08 | 0.02 | 0.08 | 0.01 | 0.10 | 0.02 | 0.08 | 0.01 | 0.03 | 0.00 | 0.06 | 0.02 | 0.04 | 0.01 | 0.11 | 0.00 | 0.01 | 0.07 | 0.03 | 0.01 | 0.00 | 0.00 | 0.01 | 0.07 | 0.07 | 0.29 | 0.40 | 0.06 | 0.12 | 0.06 | 0.18 | 0.14 | 0.51 | 0.24 | 0.01 | 0.02 | 0.00 | 0.04 | 0.00 | 0.00 | 0.08 | 0.00 | 0.01 | 0.03 | 0.01 | 0.00 | 0.05 | 0.02 | 0.03 |
| COX7B | ENSG00000131174 | 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 | 0.04 | 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 | 0.10 | 0.04 | 0.03 | 0.01 | 0.02 | 0.01 | 0.01 | 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 |
| ADGRE3 | ENSG00000131355 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.02 | 0.05 | 0.02 | 0.00 | 0.06 | 0.00 | 0.00 | 0.04 | 0.12 | 0.03 | 0.07 | 0.01 | 0.11 | 0.04 | 0.04 | 0.01 | 0.00 | 0.01 | 0.01 | 0.03 | 0.01 | 0.01 | 0.08 | 0.04 | 0.00 | 0.03 | 0.26 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.10 | 0.03 | 0.84 | 0.05 | 0.05 | 0.02 | 0.23 | 0.01 | 0.25 | 0.09 | 0.17 | 0.01 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.06 | 0.01 | 0.00 | 0.02 | 0.00 | 0.02 | 0.00 | 0.03 | 0.01 |
| CAPN7 | ENSG00000131375 | 0.00 | 0.18 | 0.00 | 0.01 | 0.07 | 0.00 | 0.01 | 0.02 | 0.28 | 0.01 | 0.00 | 0.03 | 0.01 | 0.03 | 0.03 | 0.04 | 0.01 | 0.04 | 0.02 | 0.02 | 0.04 | 0.04 | 0.05 | 0.04 | 0.01 | 0.03 | 0.03 | 0.06 | 0.01 | 0.02 | 0.06 | 0.01 | 0.00 | 0.18 | 0.07 | 0.01 | 0.00 | 0.04 | 0.00 | 0.00 | 0.14 | 0.02 | 0.16 | 0.20 | 0.01 | 0.02 | 0.05 | 0.04 | 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 | 0.03 | 0.06 |
| NAPSB | ENSG00000131401 | 0.00 | 0.00 | 0.01 | 0.02 | 0.00 | 0.00 | 0.01 | 0.01 | 0.10 | 0.04 | 0.00 | 0.02 | 0.00 | 0.06 | 0.01 | 0.07 | 0.07 | 0.11 | 0.03 | 0.02 | 0.06 | 0.03 | 0.09 | 0.03 | 0.01 | 0.03 | 0.02 | 0.03 | 0.03 | 0.05 | 0.05 | 0.04 | 0.00 | 0.07 | 0.23 | 0.02 | 0.00 | 0.03 | 0.00 | 0.00 | 0.10 | 0.04 | 0.05 | 0.32 | 0.06 | 0.07 | 0.03 | 0.06 | 0.15 | 0.13 | 0.03 | 0.17 | 0.00 | 0.04 | 0.01 | 0.00 | 0.24 | 0.03 | 0.00 | 0.15 | 0.02 | 0.13 | 0.00 | 0.00 | 0.03 | 0.02 |
| NR1H2 | ENSG00000131408 | 0.00 | 0.00 | 0.01 | 0.02 | 0.00 | 0.00 | 0.01 | 0.01 | 0.10 | 0.04 | 0.00 | 0.02 | 0.00 | 0.06 | 0.01 | 0.07 | 0.07 | 0.11 | 0.03 | 0.02 | 0.06 | 0.03 | 0.09 | 0.03 | 0.01 | 0.03 | 0.02 | 0.03 | 0.03 | 0.05 | 0.05 | 0.04 | 0.00 | 0.07 | 0.23 | 0.02 | 0.00 | 0.03 | 0.00 | 0.00 | 0.10 | 0.04 | 0.05 | 0.32 | 0.06 | 0.07 | 0.03 | 0.06 | 0.15 | 0.13 | 0.03 | 0.17 | 0.00 | 0.04 | 0.01 | 0.00 | 0.24 | 0.03 | 0.00 | 0.15 | 0.02 | 0.13 | 0.00 | 0.00 | 0.03 | 0.02 |
| LRRC4B | ENSG00000131409 | 0.00 | 0.00 | 0.01 | 0.02 | 0.00 | 0.00 | 0.01 | 0.01 | 0.11 | 0.04 | 0.00 | 0.02 | 0.00 | 0.06 | 0.02 | 0.07 | 0.07 | 0.10 | 0.03 | 0.02 | 0.06 | 0.03 | 0.08 | 0.04 | 0.02 | 0.03 | 0.02 | 0.04 | 0.03 | 0.04 | 0.04 | 0.03 | 0.00 | 0.07 | 0.23 | 0.02 | 0.00 | 0.03 | 0.00 | 0.00 | 0.11 | 0.04 | 0.06 | 0.31 | 0.06 | 0.07 | 0.03 | 0.05 | 0.15 | 0.13 | 0.02 | 0.17 | 0.00 | 0.04 | 0.01 | 0.00 | 0.17 | 0.03 | 0.00 | 0.15 | 0.03 | 0.14 | 0.00 | 0.00 | 0.03 | 0.03 |
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