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 |
| TXNDC15 | ENSG00000113621 | 0.28 | 0.01 | 0.03 | 0.01 | 0.00 | 0.00 | 0.02 | 0.04 | 0.02 | 0.05 | 0.00 | 0.00 | 0.00 | 0.04 | 0.00 | 0.07 | 0.01 | 0.05 | 0.01 | 0.05 | 0.02 | 0.05 | 0.01 | 0.08 | 0.01 | 0.04 | 0.02 | 0.04 | 0.01 | 0.03 | 0.06 | 0.04 | 0.09 | 0.01 | 0.24 | 0.02 | 0.00 | 0.06 | 0.01 | 0.00 | 0.03 | 0.04 | 0.10 | 0.16 | 0.03 | 0.01 | 0.02 | 0.02 | 0.10 | 0.01 | 0.03 | 0.04 | 0.00 | 0.00 | 0.00 | 0.10 | 0.04 | 0.00 | 0.00 | 0.03 | 0.01 | 0.02 | 0.00 | 0.03 | 0.04 | 0.10 |
| RARS | ENSG00000113643 | 0.32 | 0.01 | 0.04 | 0.01 | 0.00 | 0.00 | 0.04 | 0.01 | 0.01 | 0.11 | 0.00 | 0.00 | 0.02 | 0.06 | 0.08 | 0.04 | 0.02 | 0.04 | 0.02 | 0.06 | 0.08 | 0.02 | 0.02 | 0.04 | 0.01 | 0.03 | 0.03 | 0.06 | 0.02 | 0.02 | 0.12 | 0.02 | 0.05 | 0.01 | 0.28 | 0.02 | 0.00 | 0.03 | 0.01 | 0.00 | 0.06 | 0.04 | 0.19 | 0.15 | 0.03 | 0.02 | 0.04 | 0.03 | 0.18 | 0.01 | 0.09 | 0.07 | 0.00 | 0.00 | 0.00 | 0.04 | 0.02 | 0.00 | 0.00 | 0.08 | 0.02 | 0.05 | 0.04 | 0.00 | 0.04 | 0.10 |
| ATP6V0E1 | ENSG00000113732 | 0.33 | 0.00 | 0.05 | 0.01 | 0.00 | 0.00 | 0.04 | 0.01 | 0.03 | 0.10 | 0.00 | 0.00 | 0.02 | 0.05 | 0.09 | 0.04 | 0.02 | 0.05 | 0.02 | 0.06 | 0.07 | 0.02 | 0.03 | 0.04 | 0.02 | 0.01 | 0.04 | 0.04 | 0.03 | 0.02 | 0.13 | 0.02 | 0.05 | 0.01 | 0.39 | 0.02 | 0.00 | 0.03 | 0.01 | 0.00 | 0.09 | 0.04 | 0.22 | 0.13 | 0.03 | 0.03 | 0.05 | 0.02 | 0.21 | 0.01 | 0.14 | 0.07 | 0.00 | 0.00 | 0.00 | 0.02 | 0.02 | 0.00 | 0.01 | 0.07 | 0.03 | 0.04 | 0.04 | 0.00 | 0.04 | 0.10 |
| HRG | ENSG00000113905 | 0.05 | 0.00 | 0.03 | 0.01 | 0.00 | 0.01 | 0.03 | 0.04 | 0.19 | 0.01 | 0.00 | 0.00 | 0.00 | 0.07 | 0.14 | 0.05 | 1.57 | 0.00 | 0.61 | 0.00 | 0.70 | 0.02 | 0.22 | 0.01 | 0.04 | 0.01 | 0.06 | 0.02 | 0.03 | 0.00 | 0.13 | 0.02 | 0.12 | 0.03 | 0.10 | 0.00 | 0.00 | 0.10 | 0.00 | 0.00 | 0.19 | 0.02 | 1.05 | 0.04 | 0.62 | 0.00 | 0.33 | 0.01 | 0.78 | 0.09 | 0.12 | 0.09 | 0.24 | 0.00 | 0.00 | 0.00 | 0.06 | 0.00 | 0.02 | 0.02 | 0.12 | 0.05 | 0.00 | 0.00 | 0.03 | 0.04 |
| RBP2 | ENSG00000114113 | 0.03 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.07 | 0.02 | 0.08 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.07 | 0.01 | 0.41 | 0.00 | 0.25 | 0.00 | 0.28 | 0.02 | 0.11 | 0.01 | 0.01 | 0.00 | 0.03 | 0.01 | 0.00 | 0.00 | 0.05 | 0.00 | 0.00 | 0.03 | 0.12 | 0.01 | 0.00 | 0.05 | 0.00 | 0.00 | 0.10 | 0.02 | 0.53 | 0.03 | 0.28 | 0.00 | 0.10 | 0.00 | 0.24 | 0.02 | 0.13 | 0.06 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.02 | 0.00 | 0.01 | 0.02 | 0.03 | 0.00 | 0.00 | 0.00 | 0.04 |
| RBP1 | ENSG00000114115 | 0.03 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.07 | 0.02 | 0.08 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.07 | 0.01 | 0.42 | 0.00 | 0.25 | 0.00 | 0.28 | 0.02 | 0.11 | 0.01 | 0.01 | 0.00 | 0.03 | 0.01 | 0.00 | 0.00 | 0.05 | 0.00 | 0.00 | 0.03 | 0.11 | 0.01 | 0.00 | 0.05 | 0.00 | 0.00 | 0.10 | 0.02 | 0.53 | 0.03 | 0.28 | 0.00 | 0.10 | 0.00 | 0.24 | 0.02 | 0.13 | 0.06 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.02 | 0.00 | 0.01 | 0.02 | 0.03 | 0.00 | 0.00 | 0.00 | 0.04 |
| GRK7 | ENSG00000114124 | 0.03 | 0.01 | 0.02 | 0.01 | 0.00 | 0.00 | 0.07 | 0.02 | 0.08 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.07 | 0.01 | 0.53 | 0.01 | 0.28 | 0.00 | 0.32 | 0.01 | 0.11 | 0.02 | 0.01 | 0.01 | 0.05 | 0.00 | 0.00 | 0.00 | 0.05 | 0.01 | 0.00 | 0.03 | 0.09 | 0.01 | 0.00 | 0.05 | 0.00 | 0.00 | 0.10 | 0.02 | 0.52 | 0.03 | 0.31 | 0.01 | 0.11 | 0.00 | 0.26 | 0.02 | 0.15 | 0.07 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.02 | 0.00 | 0.01 | 0.02 | 0.04 | 0.00 | 0.00 | 0.01 | 0.05 |
| KAT2B | ENSG00000114166 | 0.00 | 0.18 | 0.00 | 0.01 | 0.07 | 0.00 | 0.01 | 0.02 | 0.22 | 0.02 | 0.00 | 0.03 | 0.02 | 0.03 | 0.02 | 0.05 | 0.01 | 0.04 | 0.01 | 0.02 | 0.02 | 0.04 | 0.05 | 0.06 | 0.02 | 0.04 | 0.03 | 0.05 | 0.03 | 0.02 | 0.06 | 0.02 | 0.03 | 0.17 | 0.06 | 0.01 | 0.00 | 0.04 | 0.00 | 0.00 | 0.09 | 0.03 | 0.11 | 0.21 | 0.01 | 0.02 | 0.04 | 0.04 | 0.05 | 0.09 | 0.12 | 0.02 | 0.05 | 0.05 | 0.00 | 0.01 | 0.00 | 0.06 | 0.03 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.05 |
| SERPINI2 | ENSG00000114204 | 0.05 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.08 | 0.01 | 0.16 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.17 | 0.01 | 1.56 | 0.00 | 0.56 | 0.00 | 0.80 | 0.00 | 0.23 | 0.00 | 0.03 | 0.01 | 0.04 | 0.01 | 0.04 | 0.00 | 0.12 | 0.01 | 0.08 | 0.01 | 0.10 | 0.00 | 0.00 | 0.06 | 0.00 | 0.00 | 0.19 | 0.01 | 1.25 | 0.02 | 0.68 | 0.00 | 0.26 | 0.01 | 0.57 | 0.00 | 0.05 | 0.11 | 0.20 | 0.00 | 0.00 | 0.00 | 0.05 | 0.00 | 0.03 | 0.01 | 0.05 | 0.02 | 0.00 | 0.00 | 0.02 | 0.03 |
| WNT5A | ENSG00000114251 | 0.00 | 0.14 | 0.00 | 0.02 | 0.00 | 0.02 | 0.00 | 0.03 | 0.04 | 0.14 | 0.00 | 0.02 | 0.00 | 0.51 | 0.00 | 0.05 | 0.01 | 0.12 | 0.00 | 0.06 | 0.00 | 0.13 | 0.01 | 0.09 | 0.00 | 0.05 | 0.02 | 0.06 | 0.00 | 0.03 | 0.01 | 0.06 | 0.00 | 0.20 | 0.06 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.17 | 0.09 | 0.18 | 0.00 | 0.10 | 0.02 | 0.08 | 0.05 | 0.36 | 0.04 | 0.14 | 0.05 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.04 | 0.00 | 0.03 | 0.05 | 0.03 |
| HYAL1 | ENSG00000114378 | 0.00 | 0.18 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.02 | 0.03 | 0.17 | 0.02 | 0.00 | 0.00 | 0.55 | 0.01 | 0.06 | 0.00 | 0.11 | 0.00 | 0.06 | 0.03 | 0.14 | 0.01 | 0.11 | 0.00 | 0.05 | 0.01 | 0.06 | 0.00 | 0.04 | 0.05 | 0.06 | 0.00 | 0.20 | 0.01 | 0.02 | 0.01 | 0.02 | 0.00 | 0.00 | 0.01 | 0.17 | 0.06 | 0.19 | 0.01 | 0.06 | 0.09 | 0.06 | 0.10 | 0.36 | 0.03 | 0.17 | 0.02 | 0.03 | 0.00 | 0.01 | 0.00 | 0.06 | 0.01 | 0.06 | 0.01 | 0.04 | 0.00 | 0.03 | 0.01 | 0.04 |
| CSPG5 | ENSG00000114646 | 0.00 | 0.18 | 0.00 | 0.02 | 0.05 | 0.00 | 0.00 | 0.04 | 0.03 | 0.13 | 0.00 | 0.04 | 0.00 | 0.55 | 0.00 | 0.06 | 0.00 | 0.09 | 0.01 | 0.05 | 0.03 | 0.08 | 0.00 | 0.11 | 0.00 | 0.05 | 0.02 | 0.06 | 0.01 | 0.05 | 0.03 | 0.05 | 0.00 | 0.24 | 0.04 | 0.02 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.16 | 0.08 | 0.21 | 0.01 | 0.05 | 0.04 | 0.05 | 0.02 | 0.24 | 0.04 | 0.13 | 0.01 | 0.04 | 0.00 | 0.01 | 0.00 | 0.14 | 0.00 | 0.05 | 0.01 | 0.04 | 0.00 | 0.03 | 0.01 | 0.05 |
| ACVR2B | ENSG00000114739 | 0.00 | 0.18 | 0.00 | 0.01 | 0.08 | 0.00 | 0.00 | 0.01 | 0.13 | 0.04 | 0.00 | 0.03 | 0.02 | 0.28 | 0.01 | 0.04 | 0.02 | 0.04 | 0.00 | 0.04 | 0.03 | 0.04 | 0.05 | 0.08 | 0.00 | 0.03 | 0.04 | 0.02 | 0.01 | 0.02 | 0.04 | 0.02 | 0.00 | 0.20 | 0.05 | 0.02 | 0.00 | 0.03 | 0.00 | 0.00 | 0.04 | 0.09 | 0.11 | 0.16 | 0.02 | 0.04 | 0.03 | 0.04 | 0.12 | 0.13 | 0.08 | 0.06 | 0.03 | 0.04 | 0.00 | 0.01 | 0.00 | 0.09 | 0.01 | 0.03 | 0.01 | 0.03 | 0.00 | 0.03 | 0.04 | 0.05 |
| AADAC | ENSG00000114771 | 0.03 | 0.01 | 0.02 | 0.01 | 0.00 | 0.00 | 0.05 | 0.01 | 0.11 | 0.01 | 0.00 | 0.00 | 0.00 | 0.05 | 0.10 | 0.01 | 0.86 | 0.01 | 0.44 | 0.00 | 0.55 | 0.02 | 0.12 | 0.00 | 0.01 | 0.00 | 0.05 | 0.01 | 0.03 | 0.01 | 0.08 | 0.01 | 0.03 | 0.03 | 0.09 | 0.01 | 0.00 | 0.06 | 0.00 | 0.00 | 0.15 | 0.01 | 0.68 | 0.02 | 0.41 | 0.01 | 0.15 | 0.01 | 0.23 | 0.07 | 0.05 | 0.09 | 0.08 | 0.01 | 0.00 | 0.00 | 0.01 | 0.08 | 0.00 | 0.01 | 0.02 | 0.03 | 0.00 | 0.00 | 0.03 | 0.04 |
| VIPR1 | ENSG00000114812 | 0.00 | 0.18 | 0.00 | 0.02 | 0.08 | 0.00 | 0.01 | 0.01 | 0.06 | 0.08 | 0.00 | 0.03 | 0.01 | 0.39 | 0.01 | 0.04 | 0.00 | 0.07 | 0.00 | 0.04 | 0.04 | 0.04 | 0.02 | 0.08 | 0.00 | 0.02 | 0.04 | 0.05 | 0.00 | 0.03 | 0.04 | 0.02 | 0.00 | 0.20 | 0.01 | 0.02 | 0.00 | 0.07 | 0.00 | 0.00 | 0.02 | 0.12 | 0.09 | 0.17 | 0.02 | 0.04 | 0.02 | 0.04 | 0.02 | 0.19 | 0.06 | 0.10 | 0.01 | 0.04 | 0.00 | 0.01 | 0.00 | 0.07 | 0.01 | 0.04 | 0.01 | 0.04 | 0.00 | 0.06 | 0.03 | 0.04 |
| NKTR | ENSG00000114857 | 0.00 | 0.18 | 0.00 | 0.02 | 0.08 | 0.00 | 0.01 | 0.01 | 0.06 | 0.08 | 0.00 | 0.03 | 0.01 | 0.39 | 0.01 | 0.04 | 0.00 | 0.07 | 0.00 | 0.04 | 0.03 | 0.04 | 0.01 | 0.08 | 0.00 | 0.02 | 0.04 | 0.05 | 0.00 | 0.03 | 0.06 | 0.02 | 0.00 | 0.20 | 0.01 | 0.02 | 0.00 | 0.03 | 0.00 | 0.00 | 0.02 | 0.12 | 0.09 | 0.17 | 0.02 | 0.04 | 0.02 | 0.04 | 0.02 | 0.19 | 0.07 | 0.10 | 0.01 | 0.04 | 0.00 | 0.01 | 0.00 | 0.12 | 0.01 | 0.04 | 0.01 | 0.04 | 0.00 | 0.03 | 0.03 | 0.04 |
| SPCS1 | ENSG00000114902 | 0.00 | 0.18 | 0.00 | 0.03 | 0.00 | 0.02 | 0.00 | 0.03 | 0.04 | 0.16 | 0.00 | 0.03 | 0.00 | 0.57 | 0.01 | 0.07 | 0.00 | 0.11 | 0.00 | 0.06 | 0.02 | 0.13 | 0.01 | 0.11 | 0.00 | 0.06 | 0.02 | 0.07 | 0.00 | 0.04 | 0.03 | 0.07 | 0.00 | 0.20 | 0.06 | 0.01 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.16 | 0.08 | 0.22 | 0.00 | 0.07 | 0.05 | 0.08 | 0.00 | 0.32 | 0.04 | 0.15 | 0.05 | 0.01 | 0.00 | 0.01 | 0.00 | 0.06 | 0.01 | 0.06 | 0.01 | 0.04 | 0.00 | 0.03 | 0.02 | 0.04 |
| SLC4A3 | ENSG00000114923 | 0.01 | 0.07 | 0.04 | 0.04 | 0.00 | 0.03 | 0.01 | 0.03 | 0.01 | 0.27 | 0.00 | 0.02 | 0.00 | 0.10 | 0.02 | 0.03 | 0.04 | 0.19 | 0.00 | 0.18 | 0.03 | 0.13 | 0.05 | 0.04 | 0.02 | 0.02 | 0.02 | 0.03 | 0.05 | 0.03 | 0.03 | 0.04 | 0.00 | 0.04 | 0.03 | 0.03 | 0.01 | 0.00 | 0.00 | 0.01 | 0.04 | 0.06 | 0.18 | 0.16 | 0.03 | 0.34 | 0.04 | 0.04 | 0.08 | 0.05 | 0.11 | 0.20 | 0.08 | 0.01 | 0.00 | 0.00 | 0.00 | 0.04 | 0.00 | 0.02 | 0.00 | 0.00 | 0.02 | 0.02 | 0.02 | 0.05 |
| TTL | ENSG00000114999 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.05 | 0.06 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.01 | 0.08 | 0.01 | 0.07 | 0.01 | 0.19 | 0.02 | 0.07 | 0.02 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.01 | 0.02 | 0.04 | 0.00 | 0.01 | 0.05 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.03 | 0.13 | 0.11 | 0.05 | 0.02 | 0.08 | 0.01 | 0.14 | 0.00 | 0.11 | 0.02 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.08 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 |
| IL1A | ENSG00000115008 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.04 | 0.06 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.01 | 0.08 | 0.01 | 0.09 | 0.01 | 0.19 | 0.02 | 0.08 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.01 | 0.03 | 0.00 | 0.01 | 0.05 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.03 | 0.14 | 0.10 | 0.05 | 0.01 | 0.13 | 0.01 | 0.14 | 0.00 | 0.12 | 0.02 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.08 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.01 |
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