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 |
| XBP1 | ENSG00000100219 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.06 | 0.14 | 0.04 | 0.00 | 0.07 | 0.00 | 0.04 | 0.04 | 0.02 | 0.15 | 0.01 | 0.04 | 0.01 | 0.03 | 0.01 | 0.03 | 0.04 | 0.02 | 0.01 | 0.02 | 0.01 | 0.00 | 0.03 | 0.01 | 0.04 | 0.00 | 0.11 | 0.01 | 0.33 | 0.00 | 0.01 | 0.00 | 0.00 | 0.05 | 0.02 | 0.15 | 0.08 | 0.03 | 0.01 | 0.07 | 0.06 | 0.26 | 0.03 | 0.04 | 0.04 | 0.10 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.04 | 0.00 | 0.00 | 0.02 | 0.07 |
| JOSD1 | ENSG00000100221 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.09 | 0.05 | 0.00 | 0.05 | 0.00 | 0.03 | 0.06 | 0.03 | 0.09 | 0.02 | 0.02 | 0.01 | 0.02 | 0.00 | 0.02 | 0.02 | 0.01 | 0.02 | 0.01 | 0.02 | 0.02 | 0.02 | 0.07 | 0.01 | 0.00 | 0.01 | 0.02 | 0.01 | 0.00 | 0.04 | 0.00 | 0.00 | 0.03 | 0.03 | 0.12 | 0.12 | 0.03 | 0.01 | 0.08 | 0.02 | 0.32 | 0.10 | 0.07 | 0.03 | 0.01 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.04 | 0.02 | 0.00 | 0.23 | 0.01 |
| CYB5R3 | ENSG00000100243 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 | 0.03 | 0.02 | 0.07 | 0.00 | 0.03 | 0.00 | 0.04 | 0.03 | 0.05 | 0.06 | 0.03 | 0.02 | 0.02 | 0.03 | 0.00 | 0.02 | 0.02 | 0.00 | 0.02 | 0.01 | 0.06 | 0.03 | 0.04 | 0.04 | 0.03 | 0.04 | 0.05 | 0.06 | 0.00 | 0.00 | 0.06 | 0.00 | 0.00 | 0.03 | 0.04 | 0.02 | 0.35 | 0.04 | 0.05 | 0.04 | 0.08 | 0.18 | 0.23 | 0.05 | 0.07 | 0.00 | 0.03 | 0.00 | 0.00 | 0.02 | 0.08 | 0.00 | 0.04 | 0.00 | 0.07 | 0.00 | 0.00 | 0.26 | 0.01 |
| HMOX1 | ENSG00000100292 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.01 | 0.01 | 0.15 | 0.03 | 0.00 | 0.04 | 0.00 | 0.02 | 0.05 | 0.04 | 0.07 | 0.01 | 0.01 | 0.01 | 0.03 | 0.04 | 0.02 | 0.02 | 0.01 | 0.01 | 0.01 | 0.01 | 0.02 | 0.01 | 0.03 | 0.01 | 0.00 | 0.01 | 0.06 | 0.02 | 0.00 | 0.02 | 0.00 | 0.00 | 0.03 | 0.03 | 0.15 | 0.09 | 0.03 | 0.01 | 0.05 | 0.02 | 0.21 | 0.07 | 0.04 | 0.04 | 0.05 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.03 | 0.00 | 0.03 | 0.00 | 0.00 | 0.09 | 0.03 |
| ARSA | ENSG00000100299 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.03 | 0.01 | 0.03 | 0.01 | 0.12 | 0.00 | 0.03 | 0.00 | 0.06 | 0.02 | 0.12 | 0.06 | 0.09 | 0.02 | 0.04 | 0.03 | 0.03 | 0.03 | 0.07 | 0.00 | 0.04 | 0.01 | 0.09 | 0.01 | 0.10 | 0.07 | 0.07 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.06 | 0.00 | 0.01 | 0.06 | 0.06 | 0.02 | 0.64 | 0.03 | 0.07 | 0.03 | 0.15 | 0.06 | 0.27 | 0.06 | 0.15 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.09 | 0.00 | 0.05 | 0.00 | 0.10 | 0.00 | 0.00 | 0.12 | 0.05 |
| TSPO | ENSG00000100300 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.00 | 0.04 | 0.01 | 0.08 | 0.00 | 0.03 | 0.00 | 0.04 | 0.04 | 0.06 | 0.07 | 0.03 | 0.01 | 0.02 | 0.04 | 0.01 | 0.02 | 0.03 | 0.00 | 0.02 | 0.02 | 0.06 | 0.03 | 0.04 | 0.04 | 0.04 | 0.00 | 0.05 | 0.02 | 0.00 | 0.00 | 0.06 | 0.00 | 0.01 | 0.05 | 0.05 | 0.01 | 0.39 | 0.04 | 0.05 | 0.03 | 0.09 | 0.10 | 0.29 | 0.04 | 0.08 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.11 | 0.00 | 0.04 | 0.00 | 0.08 | 0.00 | 0.00 | 0.20 | 0.01 |
| ACR | ENSG00000100312 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.03 | 0.01 | 0.03 | 0.01 | 0.12 | 0.00 | 0.03 | 0.00 | 0.06 | 0.02 | 0.12 | 0.06 | 0.09 | 0.02 | 0.04 | 0.03 | 0.03 | 0.03 | 0.07 | 0.00 | 0.04 | 0.01 | 0.09 | 0.01 | 0.10 | 0.07 | 0.07 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.06 | 0.00 | 0.01 | 0.06 | 0.06 | 0.02 | 0.64 | 0.03 | 0.07 | 0.03 | 0.15 | 0.06 | 0.27 | 0.06 | 0.15 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.09 | 0.00 | 0.05 | 0.00 | 0.10 | 0.00 | 0.00 | 0.12 | 0.05 |
| APOL1 | ENSG00000100342 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.02 | 0.01 | 0.11 | 0.06 | 0.00 | 0.04 | 0.00 | 0.03 | 0.06 | 0.05 | 0.07 | 0.02 | 0.01 | 0.01 | 0.04 | 0.03 | 0.02 | 0.05 | 0.01 | 0.01 | 0.01 | 0.02 | 0.02 | 0.01 | 0.03 | 0.01 | 0.00 | 0.01 | 0.02 | 0.02 | 0.00 | 0.03 | 0.00 | 0.00 | 0.02 | 0.04 | 0.11 | 0.13 | 0.03 | 0.01 | 0.05 | 0.02 | 0.39 | 0.07 | 0.05 | 0.03 | 0.03 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.04 | 0.00 | 0.00 | 0.07 | 0.03 |
| TXN2 | ENSG00000100348 | 0.00 | 0.00 | 0.00 | 0.01 | 0.03 | 0.00 | 0.02 | 0.00 | 0.10 | 0.05 | 0.00 | 0.04 | 0.00 | 0.03 | 0.07 | 0.04 | 0.07 | 0.02 | 0.01 | 0.01 | 0.04 | 0.03 | 0.02 | 0.02 | 0.01 | 0.01 | 0.01 | 0.01 | 0.03 | 0.00 | 0.03 | 0.01 | 0.00 | 0.01 | 0.02 | 0.02 | 0.00 | 0.03 | 0.00 | 0.00 | 0.03 | 0.04 | 0.09 | 0.12 | 0.03 | 0.02 | 0.05 | 0.02 | 0.38 | 0.06 | 0.08 | 0.02 | 0.03 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.04 | 0.00 | 0.00 | 0.07 | 0.03 |
| CSF2RB | ENSG00000100368 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.11 | 0.05 | 0.00 | 0.04 | 0.00 | 0.03 | 0.05 | 0.04 | 0.06 | 0.02 | 0.01 | 0.01 | 0.02 | 0.03 | 0.01 | 0.02 | 0.01 | 0.01 | 0.01 | 0.01 | 0.03 | 0.00 | 0.03 | 0.01 | 0.00 | 0.01 | 0.02 | 0.02 | 0.00 | 0.04 | 0.00 | 0.00 | 0.03 | 0.03 | 0.09 | 0.11 | 0.04 | 0.01 | 0.05 | 0.02 | 0.30 | 0.06 | 0.08 | 0.02 | 0.03 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.04 | 0.00 | 0.00 | 0.11 | 0.03 |
| UPK3A | ENSG00000100373 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.05 | 0.02 | 0.09 | 0.00 | 0.02 | 0.00 | 0.04 | 0.04 | 0.09 | 0.04 | 0.05 | 0.03 | 0.03 | 0.04 | 0.02 | 0.05 | 0.06 | 0.00 | 0.03 | 0.01 | 0.11 | 0.01 | 0.08 | 0.04 | 0.05 | 0.00 | 0.05 | 0.00 | 0.00 | 0.00 | 0.06 | 0.00 | 0.00 | 0.04 | 0.05 | 0.02 | 0.48 | 0.05 | 0.05 | 0.02 | 0.10 | 0.09 | 0.36 | 0.05 | 0.11 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.09 | 0.00 | 0.05 | 0.00 | 0.08 | 0.00 | 0.00 | 0.13 | 0.04 |
| CHADL | ENSG00000100399 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.09 | 0.00 | 0.03 | 0.00 | 0.04 | 0.03 | 0.03 | 0.06 | 0.02 | 0.03 | 0.01 | 0.03 | 0.00 | 0.02 | 0.01 | 0.01 | 0.02 | 0.01 | 0.05 | 0.04 | 0.03 | 0.05 | 0.01 | 0.04 | 0.01 | 0.09 | 0.00 | 0.00 | 0.06 | 0.00 | 0.00 | 0.03 | 0.03 | 0.02 | 0.23 | 0.04 | 0.04 | 0.04 | 0.05 | 0.17 | 0.15 | 0.08 | 0.05 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.05 | 0.00 | 0.00 | 0.32 | 0.00 |
| KCNK10 | ENSG00000100433 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.04 | 0.01 | 0.04 | 0.06 | 0.05 | 0.00 | 0.00 | 0.00 | 0.05 | 0.05 | 0.05 | 0.09 | 0.02 | 0.04 | 0.05 | 0.10 | 0.06 | 0.02 | 0.04 | 0.00 | 0.03 | 0.01 | 0.03 | 0.01 | 0.01 | 0.01 | 0.10 | 0.00 | 0.31 | 0.15 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.04 | 0.09 | 0.20 | 0.17 | 0.07 | 0.06 | 0.03 | 0.01 | 0.07 | 0.02 | 0.04 | 0.11 | 0.03 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.11 | 0.01 | 0.06 | 0.03 | 0.01 | 0.01 | 0.06 |
| CTSG | ENSG00000100448 | 0.00 | 0.00 | 0.03 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.08 | 0.06 | 0.00 | 0.00 | 0.00 | 0.02 | 0.16 | 0.02 | 0.10 | 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 | 0.07 | 0.01 | 0.00 | 0.02 | 0.26 | 0.03 | 0.00 | 0.01 | 0.00 | 0.00 | 0.09 | 0.03 | 0.19 | 0.12 | 0.03 | 0.02 | 0.05 | 0.03 | 0.06 | 0.07 | 0.20 | 0.02 | 0.01 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.03 | 0.03 | 0.01 | 0.08 | 0.00 | 0.00 | 0.03 | 0.03 |
| GZMH | ENSG00000100450 | 0.00 | 0.00 | 0.03 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.08 | 0.06 | 0.00 | 0.00 | 0.00 | 0.02 | 0.16 | 0.02 | 0.10 | 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 | 0.02 | 0.00 | 0.00 | 0.09 | 0.03 | 0.19 | 0.12 | 0.03 | 0.02 | 0.05 | 0.03 | 0.06 | 0.07 | 0.20 | 0.02 | 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 |
| GZMB | ENSG00000100453 | 0.00 | 0.00 | 0.03 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.08 | 0.06 | 0.00 | 0.00 | 0.00 | 0.02 | 0.17 | 0.02 | 0.10 | 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 | 0.02 | 0.00 | 0.00 | 0.09 | 0.03 | 0.18 | 0.12 | 0.03 | 0.02 | 0.05 | 0.03 | 0.06 | 0.07 | 0.20 | 0.02 | 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 |
| PRMT5 | ENSG00000100462 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.12 | 0.07 | 0.01 | 0.00 | 0.00 | 0.02 | 0.16 | 0.02 | 0.13 | 0.07 | 0.07 | 0.07 | 0.09 | 0.07 | 0.07 | 0.04 | 0.03 | 0.02 | 0.01 | 0.07 | 0.01 | 0.03 | 0.08 | 0.00 | 0.00 | 0.02 | 0.27 | 0.03 | 0.00 | 0.02 | 0.00 | 0.00 | 0.12 | 0.03 | 0.29 | 0.12 | 0.08 | 0.02 | 0.06 | 0.03 | 0.10 | 0.07 | 0.20 | 0.04 | 0.02 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.03 | 0.03 | 0.02 | 0.10 | 0.00 | 0.00 | 0.03 | 0.02 |
| CDKN3 | ENSG00000100526 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.02 | 0.03 | 0.00 | 0.01 | 0.00 | 0.04 | 0.10 | 0.02 | 0.06 | 0.04 | 0.04 | 0.01 | 0.13 | 0.01 | 0.07 | 0.02 | 0.01 | 0.02 | 0.01 | 0.02 | 0.01 | 0.01 | 0.04 | 0.05 | 0.05 | 0.10 | 0.06 | 0.05 | 0.01 | 0.01 | 0.00 | 0.00 | 0.07 | 0.03 | 0.06 | 0.16 | 0.01 | 0.02 | 0.02 | 0.01 | 0.00 | 0.06 | 0.03 | 0.07 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.00 | 0.01 | 0.03 | 0.01 | 0.04 | 0.00 | 0.00 | 0.01 | 0.02 |
| GSTZ1 | ENSG00000100577 | 0.01 | 0.03 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.04 | 0.05 | 0.05 | 0.00 | 0.00 | 0.00 | 0.06 | 0.03 | 0.06 | 0.05 | 0.03 | 0.05 | 0.02 | 0.08 | 0.02 | 0.03 | 0.03 | 0.00 | 0.03 | 0.01 | 0.03 | 0.01 | 0.01 | 0.00 | 0.09 | 0.00 | 0.26 | 0.06 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.02 | 0.09 | 0.18 | 0.16 | 0.05 | 0.04 | 0.06 | 0.02 | 0.06 | 0.06 | 0.08 | 0.11 | 0.03 | 0.01 | 0.00 | 0.00 | 0.04 | 0.00 | 0.00 | 0.11 | 0.02 | 0.07 | 0.03 | 0.00 | 0.00 | 0.04 |
| LGMN | ENSG00000100600 | 0.01 | 0.02 | 0.02 | 0.01 | 0.00 | 0.04 | 0.01 | 0.05 | 0.04 | 0.06 | 0.00 | 0.00 | 0.00 | 0.05 | 0.04 | 0.05 | 0.13 | 0.02 | 0.04 | 0.05 | 0.07 | 0.06 | 0.04 | 0.04 | 0.00 | 0.03 | 0.01 | 0.02 | 0.01 | 0.01 | 0.01 | 0.10 | 0.00 | 0.31 | 0.05 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.04 | 0.09 | 0.19 | 0.17 | 0.07 | 0.09 | 0.06 | 0.02 | 0.17 | 0.02 | 0.06 | 0.10 | 0.03 | 0.01 | 0.00 | 0.00 | 0.03 | 0.00 | 0.00 | 0.10 | 0.01 | 0.06 | 0.03 | 0.01 | 0.01 | 0.06 |
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