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 |
| C6 | ENSG00000039537 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.01 | 0.01 | 0.14 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.20 | 0.01 | 0.24 | 0.00 | 0.10 | 0.00 | 0.21 | 0.01 | 0.19 | 0.01 | 0.05 | 0.01 | 0.05 | 0.00 | 0.03 | 0.00 | 0.05 | 0.00 | 0.00 | 0.01 | 0.21 | 0.01 | 0.03 | 0.01 | 0.00 | 0.00 | 0.07 | 0.02 | 0.23 | 0.02 | 0.06 | 0.00 | 0.07 | 0.01 | 0.16 | 0.03 | 0.27 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.00 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.13 | 0.02 |
| PSMA4 | ENSG00000041357 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.02 | 0.00 | 0.02 | 0.03 | 0.03 | 0.00 | 0.00 | 0.09 | 0.00 | 0.03 | 0.01 | 0.09 | 0.01 | 0.03 | 0.02 | 0.07 | 0.03 | 0.07 | 0.03 | 0.03 | 0.01 | 0.03 | 0.00 | 0.04 | 0.01 | 0.05 | 0.03 | 0.05 | 0.01 | 0.06 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.10 | 0.03 | 0.18 | 0.12 | 0.12 | 0.01 | 0.03 | 0.03 | 0.13 | 0.07 | 0.06 | 0.07 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.00 | 0.01 | 0.01 | 0.01 | 0.02 | 0.00 | 0.00 | 0.14 | 0.01 |
| AIFM2 | ENSG00000042286 | 0.00 | 0.01 | 0.00 | 0.01 | 0.03 | 0.00 | 0.01 | 0.03 | 0.02 | 0.03 | 0.00 | 0.00 | 0.01 | 0.00 | 0.03 | 0.02 | 0.07 | 0.04 | 0.03 | 0.02 | 0.05 | 0.05 | 0.09 | 0.02 | 0.03 | 0.03 | 0.04 | 0.05 | 0.01 | 0.00 | 0.02 | 0.02 | 0.25 | 0.04 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.08 | 0.03 | 0.12 | 0.11 | 0.01 | 0.01 | 0.06 | 0.03 | 0.14 | 0.05 | 0.02 | 0.10 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.01 | 0.02 | 0.00 | 0.00 | 0.00 | 0.01 |
| JADE2 | ENSG00000043143 | 0.28 | 0.01 | 0.03 | 0.01 | 0.03 | 0.00 | 0.02 | 0.04 | 0.02 | 0.05 | 0.00 | 0.00 | 0.00 | 0.05 | 0.00 | 0.08 | 0.01 | 0.05 | 0.01 | 0.04 | 0.02 | 0.07 | 0.02 | 0.09 | 0.01 | 0.05 | 0.02 | 0.04 | 0.01 | 0.03 | 0.08 | 0.05 | 0.09 | 0.01 | 0.33 | 0.02 | 0.00 | 0.06 | 0.01 | 0.00 | 0.02 | 0.04 | 0.12 | 0.17 | 0.03 | 0.03 | 0.02 | 0.02 | 0.10 | 0.01 | 0.05 | 0.06 | 0.01 | 0.00 | 0.00 | 0.10 | 0.04 | 0.00 | 0.01 | 0.03 | 0.01 | 0.02 | 0.00 | 0.03 | 0.01 | 0.10 |
| ADRB1 | ENSG00000043591 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.05 | 0.02 | 0.09 | 0.00 | 0.02 | 0.01 | 0.17 | 0.06 | 0.03 | 0.04 | 0.06 | 0.01 | 0.03 | 0.03 | 0.06 | 0.08 | 0.05 | 0.01 | 0.07 | 0.01 | 0.06 | 0.01 | 0.01 | 0.01 | 0.10 | 0.11 | 0.21 | 0.09 | 0.00 | 0.01 | 0.02 | 0.00 | 0.00 | 0.04 | 0.10 | 0.18 | 0.23 | 0.01 | 0.06 | 0.03 | 0.06 | 0.04 | 0.05 | 0.04 | 0.05 | 0.07 | 0.00 | 0.00 | 0.00 | 0.00 | 0.10 | 0.00 | 0.11 | 0.00 | 0.06 | 0.00 | 0.00 | 0.01 | 0.05 |
| GUCA2B | ENSG00000044012 | 0.00 | 0.02 | 0.01 | 0.03 | 0.00 | 0.00 | 0.00 | 0.02 | 0.24 | 0.03 | 0.00 | 0.00 | 0.08 | 0.03 | 0.11 | 0.02 | 0.10 | 0.02 | 0.08 | 0.01 | 0.17 | 0.01 | 0.04 | 0.03 | 0.04 | 0.03 | 0.04 | 0.01 | 0.07 | 0.00 | 0.02 | 0.09 | 0.00 | 0.22 | 0.01 | 0.03 | 0.02 | 0.08 | 0.00 | 0.00 | 0.10 | 0.04 | 0.64 | 0.06 | 0.09 | 0.00 | 0.09 | 0.01 | 0.13 | 0.05 | 0.12 | 0.04 | 0.04 | 0.03 | 0.02 | 0.00 | 0.00 | 0.05 | 0.00 | 0.01 | 0.03 | 0.01 | 0.00 | 0.07 | 0.05 | 0.02 |
| HSPA5 | ENSG00000044574 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.05 | 0.01 | 0.03 | 0.04 | 0.00 | 0.01 | 0.00 | 0.02 | 0.04 | 0.03 | 0.05 | 0.02 | 0.06 | 0.01 | 0.10 | 0.02 | 0.07 | 0.01 | 0.01 | 0.01 | 0.04 | 0.02 | 0.00 | 0.01 | 0.03 | 0.03 | 0.06 | 0.04 | 0.08 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.09 | 0.03 | 0.12 | 0.15 | 0.04 | 0.01 | 0.02 | 0.04 | 0.02 | 0.16 | 0.08 | 0.05 | 0.01 | 0.02 | 0.01 | 0.00 | 0.05 | 0.00 | 0.02 | 0.01 | 0.03 | 0.02 | 0.00 | 0.03 | 0.03 | 0.03 |
| TNFRSF17 | ENSG00000048462 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.19 | 0.03 | 0.00 | 0.00 | 0.04 | 0.00 | 0.06 | 0.01 | 0.06 | 0.03 | 0.04 | 0.01 | 0.06 | 0.02 | 0.05 | 0.03 | 0.02 | 0.01 | 0.01 | 0.02 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.05 | 0.02 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.06 | 0.01 | 0.17 | 0.08 | 0.14 | 0.00 | 0.07 | 0.01 | 0.13 | 0.00 | 0.10 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.13 | 0.06 | 0.01 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.05 | 0.01 |
| UTS2 | ENSG00000049247 | 0.00 | 0.06 | 0.01 | 0.08 | 0.00 | 0.00 | 0.01 | 0.04 | 0.10 | 0.08 | 0.00 | 0.02 | 0.04 | 0.30 | 0.07 | 0.05 | 0.06 | 0.11 | 0.05 | 0.09 | 0.11 | 0.08 | 0.08 | 0.09 | 0.01 | 0.15 | 0.00 | 0.20 | 0.04 | 0.07 | 0.02 | 0.32 | 0.00 | 1.10 | 0.03 | 0.26 | 0.01 | 0.11 | 0.00 | 0.00 | 0.03 | 0.19 | 0.23 | 0.37 | 0.05 | 0.11 | 0.06 | 0.11 | 0.06 | 0.27 | 0.17 | 0.23 | 0.08 | 0.12 | 0.02 | 0.01 | 0.00 | 0.11 | 0.00 | 0.07 | 0.02 | 0.32 | 0.00 | 0.07 | 0.07 | 0.12 |
| TNFRSF9 | ENSG00000049249 | 0.00 | 0.06 | 0.01 | 0.08 | 0.00 | 0.00 | 0.01 | 0.04 | 0.10 | 0.08 | 0.00 | 0.03 | 0.04 | 0.30 | 0.06 | 0.05 | 0.06 | 0.11 | 0.05 | 0.08 | 0.11 | 0.08 | 0.08 | 0.09 | 0.01 | 0.15 | 0.00 | 0.20 | 0.05 | 0.07 | 0.03 | 0.31 | 0.00 | 1.10 | 0.03 | 0.26 | 0.01 | 0.11 | 0.00 | 0.00 | 0.03 | 0.19 | 0.23 | 0.37 | 0.04 | 0.11 | 0.06 | 0.11 | 0.06 | 0.27 | 0.17 | 0.23 | 0.08 | 0.12 | 0.02 | 0.01 | 0.00 | 0.11 | 0.00 | 0.07 | 0.02 | 0.33 | 0.00 | 0.07 | 0.07 | 0.12 |
| RAD51 | ENSG00000051180 | 0.00 | 0.01 | 0.00 | 0.02 | 0.14 | 0.00 | 0.01 | 0.07 | 0.02 | 0.07 | 0.00 | 0.00 | 0.00 | 0.37 | 0.01 | 0.11 | 0.01 | 0.09 | 0.02 | 0.05 | 0.04 | 0.05 | 0.01 | 0.08 | 0.01 | 0.09 | 0.00 | 0.06 | 0.01 | 0.04 | 0.01 | 0.03 | 0.00 | 0.07 | 0.02 | 0.09 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.12 | 0.04 | 0.36 | 0.00 | 0.11 | 0.03 | 0.09 | 0.05 | 0.37 | 0.04 | 0.09 | 0.01 | 0.03 | 0.00 | 0.00 | 0.00 | 0.15 | 0.00 | 0.02 | 0.01 | 0.12 | 0.00 | 0.00 | 0.01 | 0.18 |
| PRSS8 | ENSG00000052344 | 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 | 0.03 | 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 | 0.00 | 0.00 | 0.00 | 0.00 | 0.09 | 0.01 | 0.08 | 0.03 | 0.02 | 0.03 | 0.12 | 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 |
| AKR7A2 | ENSG00000053371 | 0.00 | 0.06 | 0.00 | 0.08 | 0.00 | 0.00 | 0.01 | 0.04 | 0.07 | 0.08 | 0.00 | 0.01 | 0.04 | 0.25 | 0.04 | 0.06 | 0.03 | 0.11 | 0.03 | 0.08 | 0.05 | 0.09 | 0.07 | 0.11 | 0.00 | 0.16 | 0.00 | 0.22 | 0.02 | 0.07 | 0.02 | 0.23 | 0.00 | 1.11 | 0.01 | 0.07 | 0.01 | 0.10 | 0.00 | 0.00 | 0.02 | 0.20 | 0.10 | 0.44 | 0.04 | 0.08 | 0.05 | 0.13 | 0.03 | 0.15 | 0.18 | 0.12 | 0.05 | 0.07 | 0.02 | 0.01 | 0.00 | 0.03 | 0.00 | 0.02 | 0.03 | 0.09 | 0.00 | 0.12 | 0.06 | 0.09 |
| LY75 | ENSG00000054219 | 0.02 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.02 | 0.10 | 0.12 | 0.03 | 0.00 | 0.01 | 0.00 | 0.00 | 0.05 | 0.01 | 0.10 | 0.03 | 0.04 | 0.02 | 0.11 | 0.03 | 0.03 | 0.05 | 0.01 | 0.02 | 0.01 | 0.02 | 0.04 | 0.01 | 0.06 | 0.06 | 0.00 | 0.05 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.03 | 0.34 | 0.04 | 0.04 | 0.01 | 0.08 | 0.01 | 0.06 | 0.00 | 0.05 | 0.10 | 0.03 | 0.01 | 0.00 | 0.00 | 0.00 | 0.15 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.04 | 0.01 |
| PTPRN | ENSG00000054356 | 0.01 | 0.07 | 0.04 | 0.04 | 0.00 | 0.03 | 0.01 | 0.02 | 0.01 | 0.27 | 0.00 | 0.02 | 0.00 | 0.10 | 0.03 | 0.03 | 0.04 | 0.19 | 0.00 | 0.18 | 0.03 | 0.13 | 0.05 | 0.04 | 0.02 | 0.01 | 0.02 | 0.02 | 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 | 0.06 | 0.04 | 0.08 | 0.05 | 0.09 | 0.21 | 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 | 0.04 |
| CBLN4 | ENSG00000054803 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.00 | 0.06 | 0.04 | 0.00 | 0.00 | 0.03 | 0.00 | 0.17 | 0.01 | 0.04 | 0.03 | 0.01 | 0.01 | 0.11 | 0.01 | 0.16 | 0.00 | 0.12 | 0.01 | 0.12 | 0.00 | 0.02 | 0.01 | 0.10 | 0.01 | 0.00 | 0.01 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.31 | 0.02 | 0.34 | 0.04 | 0.03 | 0.02 | 0.08 | 0.01 | 0.16 | 0.00 | 0.18 | 0.03 | 0.03 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.10 | 0.00 |
| RELT | ENSG00000054967 | 0.00 | 0.00 | 0.01 | 0.00 | 0.10 | 0.00 | 0.04 | 0.00 | 0.20 | 0.03 | 0.00 | 0.00 | 0.08 | 0.00 | 0.14 | 0.01 | 0.22 | 0.02 | 0.32 | 0.02 | 0.59 | 0.03 | 0.14 | 0.02 | 0.01 | 0.01 | 0.02 | 0.02 | 0.02 | 0.02 | 0.04 | 0.02 | 0.08 | 0.02 | 0.04 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.37 | 0.06 | 0.49 | 0.04 | 0.12 | 0.01 | 0.12 | 0.02 | 0.19 | 0.08 | 0.14 | 0.03 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.01 | 0.01 | 0.02 | 0.00 | 0.00 | 0.26 | 0.01 |
| GALC | ENSG00000054983 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.04 | 0.01 | 0.04 | 0.06 | 0.04 | 0.00 | 0.00 | 0.00 | 0.05 | 0.05 | 0.06 | 0.10 | 0.02 | 0.04 | 0.05 | 0.11 | 0.06 | 0.02 | 0.05 | 0.00 | 0.03 | 0.01 | 0.03 | 0.01 | 0.01 | 0.01 | 0.10 | 0.00 | 0.31 | 0.14 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.03 | 0.09 | 0.20 | 0.16 | 0.06 | 0.06 | 0.03 | 0.02 | 0.06 | 0.02 | 0.04 | 0.10 | 0.03 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.10 | 0.01 | 0.07 | 0.03 | 0.01 | 0.01 | 0.06 |
| MCOLN3 | ENSG00000055732 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.07 | 0.05 | 0.07 | 0.00 | 0.00 | 0.00 | 0.29 | 0.06 | 0.09 | 0.04 | 0.05 | 0.01 | 0.07 | 0.01 | 0.07 | 0.01 | 0.06 | 0.00 | 0.07 | 0.01 | 0.07 | 0.00 | 0.01 | 0.03 | 0.03 | 0.00 | 0.08 | 0.04 | 0.04 | 0.00 | 0.21 | 0.00 | 0.00 | 0.05 | 0.10 | 0.10 | 0.20 | 0.01 | 0.04 | 0.02 | 0.03 | 0.13 | 0.05 | 0.13 | 0.06 | 0.03 | 0.05 | 0.01 | 0.01 | 0.10 | 0.00 | 0.01 | 0.01 | 0.01 | 0.04 | 0.03 | 0.03 | 0.05 | 0.10 |
| ITIH4 | ENSG00000055955 | 0.00 | 0.17 | 0.00 | 0.02 | 0.00 | 0.02 | 0.00 | 0.03 | 0.03 | 0.16 | 0.00 | 0.03 | 0.00 | 0.57 | 0.01 | 0.06 | 0.00 | 0.11 | 0.00 | 0.06 | 0.05 | 0.15 | 0.01 | 0.11 | 0.00 | 0.06 | 0.02 | 0.07 | 0.00 | 0.04 | 0.03 | 0.07 | 0.00 | 0.20 | 0.08 | 0.01 | 0.00 | 0.04 | 0.00 | 0.00 | 0.01 | 0.17 | 0.08 | 0.22 | 0.00 | 0.07 | 0.03 | 0.08 | 0.00 | 0.30 | 0.03 | 0.15 | 0.05 | 0.01 | 0.00 | 0.01 | 0.00 | 0.06 | 0.01 | 0.06 | 0.01 | 0.05 | 0.00 | 0.03 | 0.02 | 0.04 |
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