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 |
| HTR2C | ENSG00000147246 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.04 | 0.03 | 0.03 | 0.00 | 0.00 | 0.06 | 0.06 | 0.01 | 0.10 | 0.01 | 0.04 | 0.01 | 0.09 | 0.02 | 0.05 | 0.04 | 0.02 | 0.01 | 0.02 | 0.01 | 0.01 | 0.00 | 0.05 | 0.01 | 0.03 | 0.01 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.02 | 0.09 | 0.06 | 0.06 | 0.01 | 0.03 | 0.01 | 0.01 | 0.02 | 0.07 | 0.09 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.02 | 0.02 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 |
| ATG4C | ENSG00000125703 | 0.00 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.07 | 0.07 | 0.05 | 0.00 | 0.02 | 0.04 | 0.01 | 0.06 | 0.06 | 0.06 | 0.04 | 0.06 | 0.03 | 0.08 | 0.05 | 0.03 | 0.04 | 0.00 | 0.06 | 0.00 | 0.05 | 0.00 | 0.01 | 0.02 | 0.04 | 0.00 | 0.13 | 0.04 | 0.01 | 0.02 | 0.18 | 0.00 | 0.00 | 0.09 | 0.07 | 0.21 | 0.12 | 0.09 | 0.02 | 0.04 | 0.02 | 0.00 | 0.06 | 0.27 | 0.02 | 0.03 | 0.05 | 0.02 | 0.01 | 0.00 | 0.03 | 0.00 | 0.01 | 0.02 | 0.01 | 0.00 | 0.07 | 0.04 | 0.04 |
| SLC22A16 | ENSG00000004809 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.29 | 0.02 | 0.12 | 0.00 | 0.01 | 0.00 | 0.13 | 0.02 | 0.06 | 0.06 | 0.05 | 0.02 | 0.03 | 0.03 | 0.07 | 0.05 | 0.07 | 0.01 | 0.03 | 0.01 | 0.04 | 0.00 | 0.03 | 0.01 | 0.08 | 0.00 | 0.15 | 0.09 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.12 | 0.09 | 0.09 | 0.24 | 0.02 | 0.02 | 0.11 | 0.02 | 0.16 | 0.03 | 0.20 | 0.06 | 0.00 | 0.04 | 0.00 | 0.00 | 0.01 | 0.25 | 0.00 | 0.02 | 0.02 | 0.06 | 0.05 | 0.03 | 0.00 | 0.12 |
| GFPT1 | ENSG00000198380 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.04 | 0.11 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.02 | 0.01 | 0.18 | 0.00 | 0.04 | 0.00 | 0.14 | 0.01 | 0.05 | 0.01 | 0.00 | 0.01 | 0.03 | 0.01 | 0.00 | 0.01 | 0.02 | 0.04 | 0.00 | 0.08 | 0.03 | 0.04 | 0.00 | 0.01 | 0.00 | 0.00 | 0.06 | 0.01 | 0.16 | 0.04 | 0.03 | 0.00 | 0.06 | 0.01 | 0.16 | 0.00 | 0.05 | 0.04 | 0.03 | 0.04 | 0.00 | 0.00 | 0.04 | 0.02 | 0.01 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.01 |
| CD40 | ENSG00000101017 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.01 | 0.10 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.04 | 0.08 | 0.01 | 0.00 | 0.01 | 0.06 | 0.00 | 0.17 | 0.00 | 0.16 | 0.00 | 0.13 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.00 | 0.01 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.16 | 0.02 | 0.22 | 0.03 | 0.02 | 0.05 | 0.09 | 0.01 | 0.36 | 0.00 | 0.10 | 0.03 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.07 | 0.01 |
| CSAD | ENSG00000139631 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.02 | 0.00 | 0.05 | 0.04 | 0.00 | 0.00 | 0.00 | 0.04 | 0.06 | 0.01 | 0.04 | 0.02 | 0.01 | 0.03 | 0.04 | 0.05 | 0.05 | 0.04 | 0.02 | 0.00 | 0.03 | 0.01 | 0.01 | 0.03 | 0.01 | 0.01 | 0.09 | 0.01 | 0.16 | 0.01 | 0.03 | 0.01 | 0.00 | 0.00 | 0.03 | 0.05 | 0.10 | 0.05 | 0.03 | 0.00 | 0.09 | 0.01 | 0.38 | 0.05 | 0.01 | 0.10 | 0.01 | 0.00 | 0.00 | 0.00 | 0.12 | 0.00 | 0.00 | 0.03 | 0.02 | 0.04 | 0.00 | 0.00 | 0.02 | 0.06 |
| MAP4K3 | ENSG00000011566 | 0.00 | 0.01 | 0.02 | 0.01 | 0.00 | 0.00 | 0.01 | 0.07 | 0.07 | 0.01 | 0.00 | 0.00 | 0.01 | 0.09 | 0.06 | 0.02 | 0.10 | 0.02 | 0.04 | 0.02 | 0.05 | 0.03 | 0.02 | 0.03 | 0.00 | 0.02 | 0.02 | 0.03 | 0.01 | 0.02 | 0.07 | 0.00 | 0.00 | 0.05 | 0.02 | 0.07 | 0.00 | 0.01 | 0.00 | 0.00 | 0.05 | 0.02 | 0.21 | 0.05 | 0.09 | 0.00 | 0.08 | 0.02 | 0.16 | 0.00 | 0.08 | 0.08 | 0.18 | 0.01 | 0.00 | 0.01 | 0.10 | 0.02 | 0.00 | 0.00 | 0.01 | 0.01 | 0.03 | 0.00 | 0.02 | 0.01 |
| GPR156 | ENSG00000175697 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.03 | 0.06 | 0.02 | 0.00 | 0.01 | 0.00 | 0.01 | 0.04 | 0.02 | 0.13 | 0.02 | 0.03 | 0.00 | 0.07 | 0.06 | 0.05 | 0.01 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.02 | 0.03 | 0.01 | 0.00 | 0.05 | 0.00 | 0.00 | 0.03 | 0.04 | 0.26 | 0.02 | 0.06 | 0.01 | 0.05 | 0.01 | 0.05 | 0.08 | 0.10 | 0.06 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.05 | 0.00 | 0.03 | 0.00 | 0.06 | 0.00 | 0.00 | 0.01 | 0.04 |
| SLC8B1 | ENSG00000089060 | 0.01 | 0.01 | 0.02 | 0.00 | 0.06 | 0.02 | 0.03 | 0.03 | 0.13 | 0.02 | 0.00 | 0.00 | 0.02 | 0.00 | 0.03 | 0.05 | 0.03 | 0.04 | 0.01 | 0.02 | 0.08 | 0.05 | 0.06 | 0.02 | 0.01 | 0.02 | 0.05 | 0.01 | 0.01 | 0.06 | 0.02 | 0.05 | 0.00 | 0.22 | 0.17 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.02 | 0.09 | 0.12 | 0.22 | 0.02 | 0.02 | 0.03 | 0.05 | 0.08 | 0.08 | 0.18 | 0.05 | 0.02 | 0.00 | 0.00 | 0.00 | 0.10 | 0.00 | 0.02 | 0.03 | 0.01 | 0.01 | 0.00 | 0.00 | 0.02 | 0.06 |
| AQP1 | ENSG00000240583 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.05 | 0.00 | 0.10 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.06 | 0.00 | 0.07 | 0.02 | 0.05 | 0.01 | 0.12 | 0.02 | 0.05 | 0.00 | 0.04 | 0.00 | 0.03 | 0.00 | 0.02 | 0.00 | 0.05 | 0.00 | 0.00 | 0.02 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.10 | 0.02 | 0.16 | 0.12 | 0.03 | 0.00 | 0.06 | 0.02 | 0.04 | 0.01 | 0.16 | 0.03 | 0.05 | 0.00 | 0.00 | 0.01 | 0.00 | 0.02 | 0.03 | 0.00 | 0.05 | 0.00 | 0.00 | 0.00 | 0.06 | 0.02 |
| PRKD3 | ENSG00000115825 | 0.00 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.06 | 0.06 | 0.01 | 0.00 | 0.00 | 0.01 | 0.05 | 0.08 | 0.01 | 0.08 | 0.02 | 0.03 | 0.01 | 0.03 | 0.03 | 0.02 | 0.03 | 0.00 | 0.01 | 0.00 | 0.03 | 0.01 | 0.03 | 0.05 | 0.01 | 0.00 | 0.05 | 0.00 | 0.04 | 0.00 | 0.01 | 0.00 | 0.00 | 0.05 | 0.02 | 0.20 | 0.05 | 0.07 | 0.00 | 0.07 | 0.02 | 0.16 | 0.00 | 0.07 | 0.06 | 0.13 | 0.01 | 0.00 | 0.00 | 0.10 | 0.06 | 0.01 | 0.01 | 0.01 | 0.01 | 0.03 | 0.00 | 0.01 | 0.01 |
| CHRNE | ENSG00000108556 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.09 | 0.05 | 0.03 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.05 | 0.02 | 0.02 | 0.02 | 0.03 | 0.05 | 0.05 | 0.01 | 0.01 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.12 | 0.02 | 0.03 | 0.02 | 0.04 | 0.00 | 0.03 | 0.00 | 0.00 | 0.03 | 0.05 | 0.11 | 0.06 | 0.01 | 0.03 | 0.03 | 0.04 | 0.19 | 0.12 | 0.17 | 0.25 | 0.00 | 0.02 | 0.00 | 0.02 | 0.00 | 0.06 | 0.00 | 0.00 | 0.00 | 0.06 | 0.00 | 0.00 | 0.06 | 0.03 |
| NLN | ENSG00000123213 | 0.00 | 0.01 | 0.00 | 0.01 | 0.05 | 0.00 | 0.00 | 0.19 | 0.01 | 0.19 | 0.00 | 0.01 | 0.00 | 0.05 | 0.01 | 0.08 | 0.02 | 0.10 | 0.02 | 0.07 | 0.02 | 0.16 | 0.01 | 0.14 | 0.00 | 0.07 | 0.03 | 0.07 | 0.00 | 0.07 | 0.01 | 0.02 | 0.00 | 0.13 | 0.13 | 0.00 | 0.00 | 0.03 | 0.00 | 0.00 | 0.02 | 0.10 | 0.03 | 0.63 | 0.00 | 0.08 | 0.01 | 0.14 | 0.06 | 0.35 | 0.04 | 0.06 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.05 | 0.03 |
| TNKS2 | ENSG00000107854 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.15 | 0.04 | 0.09 | 0.00 | 0.02 | 0.01 | 0.14 | 0.02 | 0.03 | 0.03 | 0.07 | 0.01 | 0.05 | 0.02 | 0.08 | 0.01 | 0.10 | 0.00 | 0.09 | 0.00 | 0.07 | 0.01 | 0.02 | 0.02 | 0.06 | 0.16 | 0.07 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.02 | 0.03 | 0.08 | 0.06 | 0.31 | 0.01 | 0.06 | 0.06 | 0.09 | 0.01 | 0.13 | 0.05 | 0.05 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.09 | 0.00 | 0.03 | 0.01 | 0.05 | 0.00 | 0.00 | 0.01 | 0.03 |
| UCHL5 | ENSG00000116750 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.04 | 0.19 | 0.05 | 0.02 | 0.00 | 0.08 | 0.02 | 0.11 | 0.00 | 0.07 | 0.03 | 0.05 | 0.02 | 0.12 | 0.08 | 0.05 | 0.02 | 0.04 | 0.01 | 0.10 | 0.04 | 0.03 | 0.01 | 0.18 | 0.02 | 0.18 | 0.02 | 0.09 | 0.02 | 0.01 | 0.00 | 0.01 | 0.00 | 0.18 | 0.01 | 0.29 | 0.06 | 0.07 | 0.00 | 0.05 | 0.02 | 0.15 | 0.05 | 0.13 | 0.10 | 0.06 | 0.00 | 0.01 | 0.00 | 0.30 | 0.02 | 0.00 | 0.01 | 0.02 | 0.01 | 0.06 | 0.00 | 0.15 | 0.03 |
| HIATL1 | ENSG00000148110 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.03 | 0.01 | 0.04 | 0.04 | 0.00 | 0.01 | 0.01 | 0.04 | 0.01 | 0.05 | 0.04 | 0.02 | 0.04 | 0.00 | 0.09 | 0.02 | 0.02 | 0.04 | 0.01 | 0.01 | 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 | 0.03 | 0.03 | 0.07 | 0.15 | 0.02 | 0.02 | 0.03 | 0.05 | 0.00 | 0.11 | 0.10 | 0.01 | 0.04 | 0.02 | 0.00 | 0.02 | 0.00 | 0.02 | 0.00 | 0.00 | 0.02 | 0.02 | 0.00 | 0.00 | 0.01 | 0.03 |
| MLH1 | ENSG00000076242 | 0.00 | 0.18 | 0.00 | 0.01 | 0.08 | 0.00 | 0.00 | 0.01 | 0.14 | 0.04 | 0.00 | 0.02 | 0.02 | 0.26 | 0.01 | 0.04 | 0.02 | 0.04 | 0.00 | 0.04 | 0.03 | 0.07 | 0.04 | 0.08 | 0.00 | 0.02 | 0.03 | 0.02 | 0.01 | 0.02 | 0.05 | 0.02 | 0.00 | 0.20 | 0.05 | 0.02 | 0.00 | 0.03 | 0.00 | 0.00 | 0.04 | 0.08 | 0.12 | 0.16 | 0.02 | 0.03 | 0.03 | 0.03 | 0.13 | 0.13 | 0.10 | 0.06 | 0.03 | 0.04 | 0.00 | 0.01 | 0.04 | 0.09 | 0.01 | 0.02 | 0.00 | 0.02 | 0.00 | 0.00 | 0.03 | 0.05 |
| SIRT6 | ENSG00000077463 | 0.00 | 0.01 | 0.00 | 0.02 | 0.00 | 0.04 | 0.01 | 0.03 | 0.02 | 0.13 | 0.02 | 0.00 | 0.01 | 0.10 | 0.01 | 0.08 | 0.02 | 0.12 | 0.03 | 0.11 | 0.06 | 0.11 | 0.01 | 0.09 | 0.00 | 0.04 | 0.01 | 0.10 | 0.00 | 0.06 | 0.05 | 0.13 | 0.00 | 0.03 | 0.04 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.05 | 0.11 | 0.03 | 0.82 | 0.04 | 0.19 | 0.01 | 0.27 | 0.00 | 0.74 | 0.14 | 0.07 | 0.00 | 0.00 | 0.04 | 0.00 | 0.00 | 0.03 | 0.01 | 0.02 | 0.05 | 0.01 | 0.00 | 0.05 | 0.04 | 0.06 |
| PRKAR2A | ENSG00000114302 | 0.00 | 0.18 | 0.00 | 0.02 | 0.05 | 0.00 | 0.00 | 0.03 | 0.03 | 0.16 | 0.00 | 0.03 | 0.00 | 0.55 | 0.01 | 0.06 | 0.00 | 0.10 | 0.00 | 0.06 | 0.01 | 0.12 | 0.01 | 0.11 | 0.00 | 0.04 | 0.03 | 0.10 | 0.00 | 0.04 | 0.04 | 0.05 | 0.00 | 0.24 | 0.06 | 0.03 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.16 | 0.07 | 0.20 | 0.00 | 0.06 | 0.04 | 0.05 | 0.03 | 0.31 | 0.03 | 0.16 | 0.02 | 0.03 | 0.00 | 0.01 | 0.00 | 0.13 | 0.01 | 0.06 | 0.01 | 0.04 | 0.00 | 0.03 | 0.01 | 0.05 |
| GLB1 | ENSG00000170266 | 0.00 | 0.18 | 0.00 | 0.01 | 0.08 | 0.00 | 0.01 | 0.01 | 0.16 | 0.03 | 0.00 | 0.03 | 0.02 | 0.19 | 0.01 | 0.03 | 0.02 | 0.04 | 0.00 | 0.04 | 0.07 | 0.04 | 0.06 | 0.07 | 0.00 | 0.03 | 0.03 | 0.02 | 0.01 | 0.02 | 0.06 | 0.01 | 0.00 | 0.16 | 0.05 | 0.01 | 0.01 | 0.03 | 0.00 | 0.00 | 0.06 | 0.06 | 0.12 | 0.17 | 0.04 | 0.02 | 0.04 | 0.03 | 0.15 | 0.13 | 0.11 | 0.05 | 0.05 | 0.04 | 0.00 | 0.01 | 0.04 | 0.09 | 0.02 | 0.01 | 0.00 | 0.03 | 0.00 | 0.03 | 0.02 | 0.04 |
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