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 |
| CD4 | ENSG00000010610 | 0.01 | 0.00 | 0.00 | 0.01 | 0.02 | 0.00 | 0.01 | 0.07 | 0.09 | 0.02 | 0.01 | 0.00 | 0.00 | 0.08 | 0.07 | 0.07 | 0.17 | 0.01 | 0.11 | 0.01 | 0.08 | 0.02 | 0.06 | 0.05 | 0.05 | 0.02 | 0.05 | 0.04 | 0.05 | 0.07 | 0.04 | 0.04 | 0.18 | 0.05 | 0.06 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.13 | 0.04 | 0.35 | 0.07 | 0.03 | 0.02 | 0.09 | 0.02 | 0.18 | 0.03 | 0.08 | 0.11 | 0.60 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.15 | 0.01 | 0.05 | 0.01 | 0.00 | 0.01 | 0.04 | 0.04 |
| PXDNL | ENSG00000147485 | 0.00 | 0.00 | 0.00 | 0.00 | 0.18 | 0.00 | 0.05 | 0.04 | 0.14 | 0.03 | 0.00 | 0.00 | 0.00 | 0.08 | 0.12 | 0.03 | 0.15 | 0.04 | 0.08 | 0.01 | 0.08 | 0.03 | 0.07 | 0.03 | 0.05 | 0.02 | 0.11 | 0.01 | 0.01 | 0.01 | 0.05 | 0.02 | 0.00 | 0.06 | 0.05 | 0.03 | 0.01 | 0.03 | 0.00 | 0.00 | 0.14 | 0.04 | 0.34 | 0.03 | 0.02 | 0.02 | 0.10 | 0.01 | 0.85 | 0.07 | 0.13 | 0.04 | 0.12 | 0.00 | 0.01 | 0.00 | 0.04 | 0.06 | 0.00 | 0.00 | 0.00 | 0.01 | 0.25 | 0.00 | 0.10 | 0.02 |
| SLC39A9 | ENSG00000029364 | 0.00 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.04 | 0.02 | 0.05 | 0.02 | 0.01 | 0.00 | 0.05 | 0.03 | 0.04 | 0.02 | 0.06 | 0.04 | 0.01 | 0.06 | 0.03 | 0.03 | 0.05 | 0.00 | 0.03 | 0.01 | 0.03 | 0.01 | 0.01 | 0.00 | 0.10 | 0.00 | 0.33 | 0.04 | 0.05 | 0.01 | 0.04 | 0.00 | 0.00 | 0.01 | 0.10 | 0.07 | 0.26 | 0.02 | 0.02 | 0.04 | 0.02 | 0.05 | 0.04 | 0.04 | 0.14 | 0.02 | 0.01 | 0.02 | 0.00 | 0.04 | 0.00 | 0.00 | 0.11 | 0.01 | 0.08 | 0.03 | 0.00 | 0.01 | 0.05 |
| GLUD1 | ENSG00000148672 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.19 | 0.06 | 0.08 | 0.00 | 0.02 | 0.01 | 0.12 | 0.01 | 0.03 | 0.03 | 0.08 | 0.01 | 0.07 | 0.02 | 0.12 | 0.03 | 0.12 | 0.01 | 0.09 | 0.00 | 0.07 | 0.01 | 0.02 | 0.02 | 0.07 | 0.25 | 0.02 | 0.03 | 0.01 | 0.00 | 0.01 | 0.00 | 0.01 | 0.03 | 0.09 | 0.09 | 0.27 | 0.02 | 0.07 | 0.07 | 0.09 | 0.01 | 0.12 | 0.01 | 0.09 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.06 | 0.01 | 0.03 | 0.00 | 0.05 | 0.00 | 0.00 | 0.00 | 0.04 |
| MAP2K5 | ENSG00000137764 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.00 | 0.01 | 0.02 | 0.04 | 0.02 | 0.00 | 0.00 | 0.09 | 0.00 | 0.03 | 0.02 | 0.05 | 0.02 | 0.02 | 0.03 | 0.04 | 0.04 | 0.04 | 0.04 | 0.01 | 0.01 | 0.01 | 0.05 | 0.03 | 0.02 | 0.02 | 0.02 | 0.00 | 0.01 | 0.04 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.04 | 0.13 | 0.12 | 0.07 | 0.01 | 0.02 | 0.04 | 0.07 | 0.12 | 0.15 | 0.04 | 0.01 | 0.01 | 0.00 | 0.00 | 0.06 | 0.02 | 0.01 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.09 | 0.00 |
| C9 | ENSG00000113600 | 0.00 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.02 | 0.02 | 0.12 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.21 | 0.01 | 0.25 | 0.00 | 0.09 | 0.00 | 0.15 | 0.02 | 0.20 | 0.01 | 0.06 | 0.01 | 0.05 | 0.00 | 0.02 | 0.00 | 0.06 | 0.00 | 0.00 | 0.01 | 0.31 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.08 | 0.02 | 0.25 | 0.02 | 0.08 | 0.00 | 0.08 | 0.01 | 0.16 | 0.03 | 0.31 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.08 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.15 | 0.02 |
| PTPRJ | ENSG00000149177 | 0.01 | 0.00 | 0.00 | 0.00 | 0.05 | 0.00 | 0.01 | 0.08 | 0.04 | 0.05 | 0.00 | 0.01 | 0.00 | 0.02 | 0.05 | 0.02 | 0.08 | 0.04 | 0.05 | 0.02 | 0.07 | 0.04 | 0.04 | 0.01 | 0.00 | 0.01 | 0.02 | 0.00 | 0.01 | 0.02 | 0.02 | 0.00 | 0.00 | 0.07 | 0.07 | 0.02 | 0.00 | 0.03 | 0.00 | 0.00 | 0.08 | 0.03 | 0.10 | 0.06 | 0.06 | 0.03 | 0.04 | 0.02 | 0.05 | 0.07 | 0.09 | 0.07 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.01 | 0.04 | 0.00 | 0.02 | 0.01 | 0.06 |
| DHRS1 | ENSG00000157379 | 0.00 | 0.00 | 0.03 | 0.01 | 0.00 | 0.00 | 0.01 | 0.01 | 0.09 | 0.06 | 0.00 | 0.00 | 0.00 | 0.02 | 0.15 | 0.03 | 0.09 | 0.07 | 0.05 | 0.07 | 0.11 | 0.04 | 0.05 | 0.04 | 0.02 | 0.02 | 0.01 | 0.06 | 0.00 | 0.03 | 0.08 | 0.01 | 0.00 | 0.02 | 0.26 | 0.03 | 0.00 | 0.01 | 0.00 | 0.00 | 0.10 | 0.03 | 0.18 | 0.13 | 0.03 | 0.02 | 0.05 | 0.03 | 0.27 | 0.12 | 0.22 | 0.03 | 0.01 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.03 | 0.03 | 0.01 | 0.09 | 0.00 | 0.00 | 0.03 | 0.03 |
| ELAVL1 | ENSG00000066044 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.02 | 0.00 | 0.02 | 0.06 | 0.09 | 0.00 | 0.01 | 0.04 | 0.07 | 0.02 | 0.06 | 0.08 | 0.09 | 0.04 | 0.08 | 0.03 | 0.11 | 0.02 | 0.08 | 0.01 | 0.03 | 0.00 | 0.06 | 0.02 | 0.04 | 0.02 | 0.12 | 0.00 | 0.01 | 0.07 | 0.03 | 0.01 | 0.00 | 0.00 | 0.01 | 0.07 | 0.07 | 0.35 | 0.40 | 0.10 | 0.12 | 0.10 | 0.18 | 0.14 | 0.51 | 0.25 | 0.01 | 0.02 | 0.00 | 0.04 | 0.00 | 0.00 | 0.09 | 0.00 | 0.01 | 0.03 | 0.01 | 0.02 | 0.05 | 0.03 | 0.03 |
| RHCE | ENSG00000188672 | 0.00 | 0.06 | 0.00 | 0.08 | 0.00 | 0.00 | 0.01 | 0.03 | 0.07 | 0.08 | 0.00 | 0.03 | 0.05 | 0.21 | 0.05 | 0.06 | 0.02 | 0.12 | 0.03 | 0.07 | 0.03 | 0.11 | 0.02 | 0.12 | 0.00 | 0.16 | 0.00 | 0.21 | 0.01 | 0.08 | 0.02 | 0.22 | 0.00 | 1.06 | 0.01 | 0.10 | 0.01 | 0.07 | 0.00 | 0.00 | 0.02 | 0.18 | 0.10 | 0.45 | 0.04 | 0.08 | 0.03 | 0.11 | 0.00 | 0.18 | 0.15 | 0.09 | 0.05 | 0.05 | 0.02 | 0.00 | 0.00 | 0.11 | 0.00 | 0.02 | 0.02 | 0.08 | 0.00 | 0.12 | 0.07 | 0.06 |
| FUS | ENSG00000089280 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.09 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.10 | 0.01 | 0.10 | 0.01 | 0.02 | 0.02 | 0.07 | 0.00 | 0.06 | 0.00 | 0.05 | 0.00 | 0.06 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.09 | 0.01 | 0.09 | 0.03 | 0.02 | 0.03 | 0.11 | 0.00 | 0.52 | 0.05 | 0.06 | 0.02 | 0.02 | 0.01 | 0.00 | 0.02 | 0.05 | 0.00 | 0.01 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 |
| CYB5R1 | ENSG00000159348 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.05 | 0.06 | 0.02 | 0.00 | 0.10 | 0.00 | 0.13 | 0.00 | 0.09 | 0.01 | 0.05 | 0.01 | 0.15 | 0.06 | 0.05 | 0.01 | 0.04 | 0.01 | 0.11 | 0.02 | 0.00 | 0.00 | 0.20 | 0.01 | 0.18 | 0.02 | 0.04 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.27 | 0.00 | 0.31 | 0.07 | 0.06 | 0.00 | 0.10 | 0.01 | 0.10 | 0.00 | 0.11 | 0.12 | 0.05 | 0.00 | 0.01 | 0.00 | 0.26 | 0.02 | 0.02 | 0.01 | 0.11 | 0.00 | 0.09 | 0.00 | 0.18 | 0.01 |
| SIRT1 | ENSG00000096717 | 0.00 | 0.00 | 0.00 | 0.01 | 0.03 | 0.00 | 0.02 | 0.03 | 0.01 | 0.04 | 0.00 | 0.00 | 0.03 | 0.00 | 0.04 | 0.03 | 0.06 | 0.03 | 0.03 | 0.02 | 0.05 | 0.05 | 0.08 | 0.02 | 0.03 | 0.03 | 0.07 | 0.03 | 0.01 | 0.00 | 0.02 | 0.03 | 0.25 | 0.04 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.07 | 0.04 | 0.11 | 0.11 | 0.00 | 0.01 | 0.04 | 0.03 | 0.09 | 0.05 | 0.02 | 0.12 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.01 |
| SLC35A3 | ENSG00000117620 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.07 | 0.03 | 0.06 | 0.00 | 0.00 | 0.00 | 0.39 | 0.02 | 0.12 | 0.02 | 0.09 | 0.01 | 0.08 | 0.02 | 0.09 | 0.02 | 0.07 | 0.00 | 0.07 | 0.01 | 0.06 | 0.00 | 0.02 | 0.03 | 0.04 | 0.00 | 0.11 | 0.04 | 0.04 | 0.00 | 0.25 | 0.00 | 0.00 | 0.03 | 0.11 | 0.15 | 0.17 | 0.00 | 0.07 | 0.03 | 0.02 | 0.02 | 0.06 | 0.06 | 0.09 | 0.03 | 0.05 | 0.01 | 0.00 | 0.00 | 0.07 | 0.01 | 0.01 | 0.01 | 0.03 | 0.00 | 0.03 | 0.04 | 0.11 |
| SETD1B | ENSG00000139718 | 0.01 | 0.01 | 0.03 | 0.00 | 0.07 | 0.02 | 0.03 | 0.06 | 0.10 | 0.04 | 0.00 | 0.00 | 0.01 | 0.02 | 0.03 | 0.05 | 0.03 | 0.07 | 0.02 | 0.03 | 0.08 | 0.05 | 0.06 | 0.04 | 0.01 | 0.01 | 0.04 | 0.03 | 0.00 | 0.06 | 0.04 | 0.08 | 0.00 | 0.17 | 0.08 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.04 | 0.09 | 0.15 | 0.24 | 0.01 | 0.02 | 0.05 | 0.08 | 0.09 | 0.23 | 0.19 | 0.06 | 0.01 | 0.00 | 0.00 | 0.00 | 0.07 | 0.06 | 0.03 | 0.01 | 0.02 | 0.01 | 0.00 | 0.00 | 0.03 | 0.06 |
| NTSR1 | ENSG00000101188 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.04 | 0.01 | 0.06 | 0.04 | 0.00 | 0.01 | 0.03 | 0.00 | 0.28 | 0.01 | 0.07 | 0.04 | 0.02 | 0.01 | 0.11 | 0.01 | 0.18 | 0.00 | 0.10 | 0.01 | 0.12 | 0.01 | 0.03 | 0.00 | 0.11 | 0.00 | 0.00 | 0.01 | 0.05 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.34 | 0.02 | 0.49 | 0.04 | 0.04 | 0.03 | 0.15 | 0.01 | 0.27 | 0.00 | 0.21 | 0.06 | 0.02 | 0.02 | 0.03 | 0.00 | 0.04 | 0.00 | 0.02 | 0.00 | 0.01 | 0.02 | 0.00 | 0.00 | 0.13 | 0.00 |
| PCDH15 | ENSG00000150275 | 0.00 | 0.01 | 0.00 | 0.02 | 0.03 | 0.00 | 0.02 | 0.06 | 0.05 | 0.07 | 0.07 | 0.00 | 0.01 | 0.05 | 0.03 | 0.03 | 0.06 | 0.05 | 0.06 | 0.03 | 0.11 | 0.10 | 0.04 | 0.03 | 0.01 | 0.05 | 0.00 | 0.01 | 0.01 | 0.01 | 0.02 | 0.02 | 0.09 | 0.01 | 0.04 | 0.04 | 0.01 | 0.01 | 0.00 | 0.02 | 0.08 | 0.04 | 0.13 | 0.17 | 0.03 | 0.03 | 0.03 | 0.06 | 0.33 | 0.12 | 0.03 | 0.11 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.01 | 0.05 | 0.00 | 0.00 | 0.00 | 0.07 |
| KAT2A | ENSG00000108773 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.08 | 0.05 | 0.02 | 0.00 | 0.00 | 0.01 | 0.02 | 0.06 | 0.01 | 0.03 | 0.05 | 0.02 | 0.01 | 0.19 | 0.04 | 0.15 | 0.03 | 0.05 | 0.01 | 0.04 | 0.02 | 0.03 | 0.03 | 0.03 | 0.04 | 0.02 | 0.01 | 0.02 | 0.16 | 0.02 | 0.12 | 0.00 | 0.00 | 0.05 | 0.10 | 0.02 | 0.15 | 0.07 | 0.04 | 0.03 | 0.07 | 0.00 | 0.20 | 0.05 | 0.10 | 0.01 | 0.01 | 0.00 | 0.02 | 0.04 | 0.00 | 0.00 | 0.01 | 0.01 | 0.03 | 0.00 | 0.05 | 0.01 | 0.03 |
| ATF1 | ENSG00000123268 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.01 | 0.12 | 0.03 | 0.00 | 0.00 | 0.00 | 0.04 | 0.04 | 0.02 | 0.02 | 0.02 | 0.01 | 0.03 | 0.08 | 0.04 | 0.04 | 0.04 | 0.02 | 0.00 | 0.03 | 0.01 | 0.01 | 0.05 | 0.03 | 0.01 | 0.09 | 0.05 | 0.21 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.04 | 0.05 | 0.11 | 0.05 | 0.04 | 0.00 | 0.05 | 0.01 | 0.26 | 0.04 | 0.13 | 0.09 | 0.02 | 0.00 | 0.00 | 0.00 | 0.12 | 0.02 | 0.02 | 0.03 | 0.02 | 0.05 | 0.00 | 0.00 | 0.03 | 0.06 |
| EBPL | ENSG00000123179 | 0.00 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.39 | 0.06 | 0.31 | 0.00 | 0.00 | 0.00 | 0.14 | 0.03 | 0.06 | 0.01 | 0.12 | 0.02 | 0.12 | 0.09 | 0.07 | 0.12 | 0.03 | 0.10 | 0.02 | 0.11 | 0.04 | 0.01 | 0.02 | 0.00 | 0.27 | 0.00 | 0.09 | 0.00 | 0.07 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.14 | 0.03 | 0.24 | 0.01 | 0.21 | 0.01 | 0.04 | 0.03 | 0.19 | 0.01 | 0.51 | 0.03 | 0.02 | 0.00 | 0.00 | 0.03 | 0.12 | 0.00 | 0.09 | 0.00 | 0.17 | 0.00 | 0.00 | 0.02 | 0.04 |
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