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 |
| OR5AU1 | ENSG00000169327 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.02 | 0.09 | 0.06 | 0.00 | 0.00 | 0.00 | 0.05 | 0.14 | 0.03 | 0.14 | 0.08 | 0.10 | 0.06 | 0.09 | 0.07 | 0.09 | 0.05 | 0.03 | 0.02 | 0.01 | 0.08 | 0.01 | 0.05 | 0.09 | 0.00 | 0.00 | 0.02 | 0.27 | 0.03 | 0.01 | 0.02 | 0.00 | 0.00 | 0.09 | 0.03 | 0.40 | 0.10 | 0.07 | 0.01 | 0.09 | 0.03 | 0.16 | 0.10 | 0.17 | 0.09 | 0.03 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.03 | 0.02 | 0.01 | 0.09 | 0.00 | 0.00 | 0.03 | 0.02 |
| UMOD | ENSG00000169344 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.10 | 0.03 | 0.00 | 0.00 | 0.01 | 0.02 | 0.03 | 0.01 | 0.04 | 0.02 | 0.02 | 0.02 | 0.03 | 0.02 | 0.02 | 0.01 | 0.03 | 0.01 | 0.02 | 0.01 | 0.00 | 0.00 | 0.03 | 0.01 | 0.00 | 0.01 | 0.02 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.04 | 0.01 | 0.13 | 0.04 | 0.05 | 0.00 | 0.07 | 0.01 | 0.09 | 0.00 | 0.02 | 0.02 | 0.01 | 0.01 | 0.00 | 0.00 | 0.06 | 0.00 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.01 | 0.01 |
| GP2 | ENSG00000169347 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.10 | 0.03 | 0.00 | 0.00 | 0.01 | 0.02 | 0.03 | 0.01 | 0.04 | 0.02 | 0.02 | 0.02 | 0.03 | 0.02 | 0.02 | 0.01 | 0.03 | 0.01 | 0.02 | 0.01 | 0.00 | 0.00 | 0.03 | 0.01 | 0.00 | 0.01 | 0.02 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.04 | 0.01 | 0.13 | 0.04 | 0.05 | 0.00 | 0.07 | 0.01 | 0.09 | 0.00 | 0.02 | 0.02 | 0.01 | 0.01 | 0.00 | 0.00 | 0.06 | 0.00 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.01 | 0.01 |
| SLC33A1 | ENSG00000169359 | 0.05 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.04 | 0.02 | 0.10 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.13 | 0.01 | 0.89 | 0.00 | 0.47 | 0.01 | 0.60 | 0.02 | 0.15 | 0.01 | 0.02 | 0.00 | 0.05 | 0.01 | 0.04 | 0.00 | 0.08 | 0.01 | 0.03 | 0.01 | 0.10 | 0.01 | 0.00 | 0.06 | 0.00 | 0.00 | 0.15 | 0.01 | 0.72 | 0.02 | 0.47 | 0.01 | 0.17 | 0.01 | 0.21 | 0.02 | 0.05 | 0.08 | 0.10 | 0.00 | 0.00 | 0.00 | 0.01 | 0.05 | 0.01 | 0.01 | 0.02 | 0.03 | 0.00 | 0.00 | 0.01 | 0.03 |
| RNASE2 | ENSG00000169385 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.02 | 0.09 | 0.06 | 0.00 | 0.00 | 0.00 | 0.05 | 0.14 | 0.03 | 0.14 | 0.08 | 0.11 | 0.06 | 0.09 | 0.07 | 0.09 | 0.04 | 0.03 | 0.02 | 0.01 | 0.08 | 0.01 | 0.05 | 0.09 | 0.00 | 0.00 | 0.02 | 0.29 | 0.03 | 0.01 | 0.02 | 0.00 | 0.00 | 0.09 | 0.03 | 0.43 | 0.10 | 0.07 | 0.02 | 0.09 | 0.03 | 0.16 | 0.08 | 0.18 | 0.08 | 0.02 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.02 | 0.03 | 0.10 | 0.00 | 0.00 | 0.03 | 0.02 |
| ELSPBP1 | ENSG00000169393 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.04 | 0.07 | 0.04 | 0.00 | 0.02 | 0.00 | 0.08 | 0.01 | 0.08 | 0.04 | 0.10 | 0.02 | 0.02 | 0.10 | 0.05 | 0.05 | 0.03 | 0.01 | 0.02 | 0.01 | 0.04 | 0.02 | 0.05 | 0.03 | 0.04 | 0.00 | 0.07 | 0.13 | 0.02 | 0.00 | 0.03 | 0.00 | 0.00 | 0.04 | 0.06 | 0.04 | 0.32 | 0.06 | 0.07 | 0.03 | 0.06 | 0.06 | 0.22 | 0.02 | 0.17 | 0.00 | 0.04 | 0.01 | 0.00 | 0.07 | 0.03 | 0.01 | 0.13 | 0.02 | 0.13 | 0.00 | 0.00 | 0.02 | 0.02 |
| RNASE3 | ENSG00000169397 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.02 | 0.09 | 0.06 | 0.00 | 0.00 | 0.00 | 0.05 | 0.15 | 0.03 | 0.16 | 0.08 | 0.10 | 0.06 | 0.09 | 0.07 | 0.09 | 0.04 | 0.03 | 0.02 | 0.01 | 0.08 | 0.01 | 0.05 | 0.09 | 0.00 | 0.00 | 0.02 | 0.29 | 0.03 | 0.01 | 0.02 | 0.00 | 0.00 | 0.09 | 0.03 | 0.42 | 0.10 | 0.07 | 0.02 | 0.08 | 0.03 | 0.16 | 0.08 | 0.16 | 0.08 | 0.02 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.02 | 0.03 | 0.10 | 0.00 | 0.00 | 0.03 | 0.02 |
| RNASE6 | ENSG00000169413 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.02 | 0.09 | 0.06 | 0.00 | 0.00 | 0.00 | 0.05 | 0.15 | 0.03 | 0.16 | 0.08 | 0.10 | 0.06 | 0.10 | 0.07 | 0.10 | 0.04 | 0.03 | 0.02 | 0.01 | 0.08 | 0.01 | 0.05 | 0.09 | 0.00 | 0.00 | 0.02 | 0.29 | 0.03 | 0.01 | 0.02 | 0.00 | 0.00 | 0.09 | 0.03 | 0.41 | 0.10 | 0.07 | 0.02 | 0.08 | 0.03 | 0.15 | 0.08 | 0.17 | 0.08 | 0.02 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.02 | 0.02 | 0.10 | 0.00 | 0.00 | 0.03 | 0.02 |
| NPR1 | ENSG00000169418 | 0.03 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.06 | 0.00 | 0.43 | 0.01 | 0.02 | 0.00 | 0.11 | 0.00 | 0.38 | 0.00 | 0.27 | 0.00 | 0.05 | 0.01 | 0.25 | 0.01 | 0.19 | 0.00 | 0.02 | 0.00 | 0.15 | 0.00 | 0.06 | 0.00 | 0.36 | 0.00 | 0.49 | 0.01 | 0.14 | 0.02 | 0.11 | 0.00 | 0.01 | 0.00 | 0.31 | 0.00 | 0.58 | 0.02 | 0.19 | 0.00 | 0.22 | 0.00 | 0.53 | 0.00 | 0.46 | 0.01 | 0.12 | 0.00 | 0.00 | 0.00 | 0.25 | 0.04 | 0.01 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.20 | 0.00 |
| KCNK9 | ENSG00000169427 | 0.03 | 0.00 | 0.02 | 0.00 | 0.06 | 0.00 | 0.06 | 0.03 | 0.19 | 0.03 | 0.02 | 0.00 | 0.10 | 0.01 | 0.27 | 0.01 | 0.34 | 0.01 | 0.27 | 0.00 | 0.49 | 0.01 | 0.21 | 0.02 | 0.15 | 0.02 | 0.21 | 0.02 | 0.14 | 0.02 | 0.34 | 0.01 | 0.25 | 0.02 | 0.04 | 0.00 | 0.02 | 0.02 | 0.00 | 0.01 | 0.42 | 0.05 | 1.48 | 0.04 | 0.21 | 0.00 | 0.11 | 0.02 | 0.24 | 0.03 | 0.19 | 0.07 | 0.03 | 0.03 | 0.02 | 0.00 | 0.25 | 0.01 | 0.17 | 0.03 | 0.03 | 0.03 | 0.50 | 0.00 | 0.23 | 0.02 |
| CXCL8 | ENSG00000169429 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.01 | 0.19 | 0.02 | 0.00 | 0.00 | 0.00 | 0.06 | 0.07 | 0.02 | 0.23 | 0.01 | 0.10 | 0.01 | 0.20 | 0.02 | 0.07 | 0.01 | 0.02 | 0.01 | 0.05 | 0.01 | 0.01 | 0.00 | 0.02 | 0.08 | 0.00 | 0.03 | 0.07 | 0.00 | 0.02 | 0.02 | 0.00 | 0.00 | 0.16 | 0.02 | 0.31 | 0.11 | 0.08 | 0.03 | 0.04 | 0.01 | 0.05 | 0.05 | 0.07 | 0.06 | 0.10 | 0.01 | 0.01 | 0.01 | 0.00 | 0.03 | 0.00 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.03 |
| CD52 | ENSG00000169442 | 0.00 | 0.06 | 0.00 | 0.08 | 0.00 | 0.00 | 0.01 | 0.02 | 0.06 | 0.11 | 0.00 | 0.01 | 0.05 | 0.19 | 0.04 | 0.07 | 0.02 | 0.12 | 0.02 | 0.07 | 0.01 | 0.14 | 0.02 | 0.15 | 0.00 | 0.18 | 0.01 | 0.22 | 0.00 | 0.10 | 0.00 | 0.21 | 0.00 | 1.06 | 0.01 | 0.10 | 0.01 | 0.07 | 0.00 | 0.00 | 0.02 | 0.18 | 0.08 | 0.45 | 0.04 | 0.08 | 0.02 | 0.13 | 0.14 | 0.18 | 0.14 | 0.10 | 0.04 | 0.06 | 0.02 | 0.00 | 0.00 | 0.07 | 0.00 | 0.02 | 0.02 | 0.08 | 0.00 | 0.12 | 0.05 | 0.06 |
| OR4K14 | ENSG00000169484 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.00 | 0.01 | 0.02 | 0.10 | 0.05 | 0.00 | 0.00 | 0.00 | 0.05 | 0.16 | 0.04 | 0.20 | 0.07 | 0.09 | 0.06 | 0.11 | 0.07 | 0.07 | 0.04 | 0.03 | 0.02 | 0.01 | 0.09 | 0.01 | 0.04 | 0.08 | 0.00 | 0.00 | 0.02 | 0.13 | 0.03 | 0.01 | 0.02 | 0.00 | 0.00 | 0.10 | 0.03 | 0.40 | 0.12 | 0.07 | 0.02 | 0.08 | 0.03 | 0.21 | 0.08 | 0.17 | 0.09 | 0.02 | 0.01 | 0.00 | 0.01 | 0.01 | 0.00 | 0.02 | 0.03 | 0.01 | 0.09 | 0.00 | 0.00 | 0.03 | 0.03 |
| OR4K15 | ENSG00000169488 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.00 | 0.01 | 0.02 | 0.10 | 0.05 | 0.00 | 0.00 | 0.00 | 0.05 | 0.16 | 0.04 | 0.20 | 0.07 | 0.09 | 0.06 | 0.11 | 0.07 | 0.07 | 0.04 | 0.03 | 0.02 | 0.01 | 0.09 | 0.01 | 0.04 | 0.08 | 0.00 | 0.00 | 0.02 | 0.13 | 0.03 | 0.01 | 0.02 | 0.00 | 0.00 | 0.10 | 0.03 | 0.40 | 0.12 | 0.07 | 0.02 | 0.08 | 0.03 | 0.21 | 0.08 | 0.17 | 0.09 | 0.02 | 0.01 | 0.00 | 0.01 | 0.01 | 0.00 | 0.02 | 0.03 | 0.01 | 0.09 | 0.00 | 0.00 | 0.03 | 0.03 |
| GPR183 | ENSG00000169508 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.06 | 0.17 | 0.03 | 0.00 | 0.01 | 0.01 | 0.06 | 0.11 | 0.04 | 0.08 | 0.04 | 0.09 | 0.03 | 0.09 | 0.04 | 0.14 | 0.03 | 0.08 | 0.01 | 0.14 | 0.01 | 0.02 | 0.02 | 0.26 | 0.02 | 0.06 | 0.01 | 0.03 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.13 | 0.05 | 0.25 | 0.09 | 0.18 | 0.02 | 0.05 | 0.02 | 0.38 | 0.05 | 0.21 | 0.12 | 0.01 | 0.01 | 0.00 | 0.00 | 0.02 | 0.07 | 0.03 | 0.02 | 0.04 | 0.04 | 0.05 | 0.00 | 0.07 | 0.05 |
| MUC15 | ENSG00000169550 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.06 | 0.06 | 0.00 | 0.00 | 0.00 | 0.04 | 0.05 | 0.03 | 0.04 | 0.04 | 0.02 | 0.03 | 0.14 | 0.02 | 0.05 | 0.02 | 0.02 | 0.01 | 0.00 | 0.02 | 0.01 | 0.02 | 0.03 | 0.00 | 0.00 | 0.01 | 0.02 | 0.01 | 0.02 | 0.03 | 0.00 | 0.00 | 0.07 | 0.04 | 0.11 | 0.13 | 0.00 | 0.04 | 0.05 | 0.03 | 0.01 | 0.11 | 0.06 | 0.08 | 0.01 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.02 |
| GJB1 | ENSG00000169562 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.05 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.02 | 0.03 | 0.04 | 0.02 | 0.01 | 0.09 | 0.02 | 0.02 | 0.02 | 0.01 | 0.01 | 0.00 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.02 | 0.14 | 0.03 | 0.03 | 0.01 | 0.04 | 0.01 | 0.18 | 0.00 | 0.16 | 0.08 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.02 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 |
| VPREB1 | ENSG00000169575 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.02 | 0.21 | 0.04 | 0.03 | 0.01 | 0.03 | 0.05 | 0.14 | 0.03 | 0.26 | 0.03 | 0.09 | 0.01 | 0.06 | 0.02 | 0.06 | 0.02 | 0.02 | 0.01 | 0.05 | 0.05 | 0.00 | 0.04 | 0.01 | 0.04 | 0.03 | 0.05 | 0.06 | 0.06 | 0.00 | 0.01 | 0.00 | 0.00 | 0.06 | 0.04 | 0.24 | 0.08 | 0.04 | 0.00 | 0.07 | 0.03 | 0.32 | 0.03 | 0.18 | 0.05 | 0.25 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.03 | 0.03 | 0.00 | 0.00 | 0.12 | 0.03 |
| GKN1 | ENSG00000169605 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.04 | 0.11 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.03 | 0.01 | 0.18 | 0.00 | 0.05 | 0.00 | 0.07 | 0.00 | 0.03 | 0.01 | 0.00 | 0.01 | 0.01 | 0.01 | 0.00 | 0.01 | 0.02 | 0.03 | 0.06 | 0.02 | 0.03 | 0.04 | 0.00 | 0.01 | 0.00 | 0.00 | 0.05 | 0.01 | 0.15 | 0.04 | 0.03 | 0.00 | 0.05 | 0.01 | 0.13 | 0.00 | 0.05 | 0.05 | 0.03 | 0.05 | 0.00 | 0.00 | 0.04 | 0.02 | 0.00 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.01 |
| PROKR1 | ENSG00000169618 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.04 | 0.09 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.02 | 0.01 | 0.18 | 0.00 | 0.05 | 0.00 | 0.07 | 0.00 | 0.03 | 0.02 | 0.00 | 0.01 | 0.01 | 0.01 | 0.00 | 0.01 | 0.02 | 0.03 | 0.06 | 0.02 | 0.06 | 0.04 | 0.00 | 0.01 | 0.00 | 0.00 | 0.05 | 0.01 | 0.15 | 0.04 | 0.03 | 0.00 | 0.05 | 0.01 | 0.13 | 0.00 | 0.07 | 0.04 | 0.03 | 0.05 | 0.00 | 0.00 | 0.04 | 0.02 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.01 | 0.01 |
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