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 |
| ITIH1 | ENSG00000055957 | 0.00 | 0.17 | 0.00 | 0.02 | 0.00 | 0.02 | 0.00 | 0.03 | 0.03 | 0.15 | 0.00 | 0.03 | 0.00 | 0.57 | 0.01 | 0.06 | 0.00 | 0.11 | 0.00 | 0.06 | 0.05 | 0.13 | 0.01 | 0.11 | 0.00 | 0.06 | 0.02 | 0.07 | 0.00 | 0.03 | 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 | 0.21 | 0.00 | 0.07 | 0.04 | 0.08 | 0.00 | 0.30 | 0.04 | 0.15 | 0.05 | 0.01 | 0.00 | 0.01 | 0.00 | 0.06 | 0.01 | 0.06 | 0.01 | 0.04 | 0.00 | 0.03 | 0.02 | 0.04 |
| IL17RB | ENSG00000056736 | 0.00 | 0.15 | 0.00 | 0.02 | 0.00 | 0.02 | 0.00 | 0.03 | 0.03 | 0.16 | 0.00 | 0.03 | 0.00 | 0.54 | 0.01 | 0.06 | 0.00 | 0.11 | 0.00 | 0.06 | 0.02 | 0.16 | 0.00 | 0.10 | 0.00 | 0.05 | 0.02 | 0.07 | 0.00 | 0.04 | 0.01 | 0.07 | 0.00 | 0.20 | 0.06 | 0.01 | 0.02 | 0.03 | 0.00 | 0.00 | 0.00 | 0.16 | 0.07 | 0.20 | 0.00 | 0.07 | 0.01 | 0.08 | 0.00 | 0.40 | 0.04 | 0.14 | 0.05 | 0.01 | 0.00 | 0.01 | 0.00 | 0.06 | 0.01 | 0.05 | 0.00 | 0.04 | 0.00 | 0.03 | 0.04 | 0.03 |
| SERPINB3 | ENSG00000057149 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.10 | 0.02 | 0.09 | 0.00 | 0.00 | 0.00 | 0.02 | 0.03 | 0.09 | 0.05 | 0.06 | 0.02 | 0.14 | 0.05 | 0.20 | 0.02 | 0.16 | 0.00 | 0.12 | 0.01 | 0.11 | 0.00 | 0.08 | 0.02 | 0.06 | 0.00 | 0.10 | 0.01 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.08 | 0.05 | 0.09 | 0.33 | 0.05 | 0.03 | 0.00 | 0.07 | 0.01 | 0.11 | 0.13 | 0.07 | 0.00 | 0.07 | 0.00 | 0.00 | 0.10 | 0.00 | 0.01 | 0.02 | 0.00 | 0.04 | 0.00 | 0.01 | 0.03 | 0.01 |
| F7 | ENSG00000057593 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.04 | 0.22 | 0.01 | 0.00 | 0.01 | 0.01 | 0.02 | 0.12 | 0.07 | 0.21 | 0.05 | 0.15 | 0.01 | 0.22 | 0.03 | 0.14 | 0.03 | 0.11 | 0.01 | 0.17 | 0.02 | 0.02 | 0.02 | 0.29 | 0.00 | 0.06 | 0.04 | 0.13 | 0.03 | 0.02 | 0.00 | 0.00 | 0.00 | 0.16 | 0.05 | 0.26 | 0.14 | 0.23 | 0.01 | 0.09 | 0.03 | 0.33 | 0.12 | 0.44 | 0.10 | 0.01 | 0.04 | 0.00 | 0.00 | 0.02 | 0.12 | 0.04 | 0.02 | 0.05 | 0.02 | 0.08 | 0.00 | 0.07 | 0.07 |
| RIOK2 | ENSG00000058729 | 0.06 | 0.01 | 0.02 | 0.01 | 0.00 | 0.01 | 0.01 | 0.17 | 0.02 | 0.08 | 0.00 | 0.01 | 0.00 | 0.03 | 0.01 | 0.07 | 0.01 | 0.08 | 0.00 | 0.07 | 0.03 | 0.09 | 0.01 | 0.12 | 0.00 | 0.12 | 0.01 | 0.02 | 0.00 | 0.05 | 0.03 | 0.03 | 0.00 | 0.02 | 0.12 | 0.02 | 0.00 | 0.05 | 0.00 | 0.00 | 0.02 | 0.07 | 0.08 | 0.48 | 0.00 | 0.05 | 0.03 | 0.06 | 0.00 | 0.13 | 0.04 | 0.04 | 0.01 | 0.02 | 0.00 | 0.07 | 0.04 | 0.00 | 0.01 | 0.02 | 0.00 | 0.02 | 0.00 | 0.00 | 0.05 | 0.03 |
| SLC2A3 | ENSG00000059804 | 0.01 | 0.01 | 0.00 | 0.01 | 0.02 | 0.00 | 0.01 | 0.07 | 0.09 | 0.03 | 0.01 | 0.00 | 0.00 | 0.05 | 0.06 | 0.07 | 0.13 | 0.01 | 0.11 | 0.02 | 0.10 | 0.02 | 0.04 | 0.07 | 0.04 | 0.03 | 0.08 | 0.03 | 0.05 | 0.07 | 0.02 | 0.05 | 0.14 | 0.05 | 0.05 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.11 | 0.04 | 0.31 | 0.08 | 0.03 | 0.02 | 0.03 | 0.03 | 0.00 | 0.03 | 0.14 | 0.11 | 0.57 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.12 | 0.01 | 0.03 | 0.02 | 0.00 | 0.01 | 0.04 | 0.04 |
| GUCY1B3 | ENSG00000061918 | 0.01 | 0.02 | 0.00 | 0.02 | 0.06 | 0.02 | 0.02 | 0.04 | 0.06 | 0.13 | 0.00 | 0.02 | 0.00 | 0.01 | 0.04 | 0.06 | 0.02 | 0.11 | 0.02 | 0.09 | 0.05 | 0.07 | 0.05 | 0.07 | 0.01 | 0.06 | 0.02 | 0.03 | 0.03 | 0.03 | 0.06 | 0.06 | 0.00 | 0.12 | 0.10 | 0.05 | 0.00 | 0.03 | 0.00 | 0.00 | 0.06 | 0.07 | 0.06 | 0.26 | 0.02 | 0.08 | 0.02 | 0.05 | 0.10 | 0.05 | 0.11 | 0.12 | 0.02 | 0.01 | 0.00 | 0.00 | 0.03 | 0.03 | 0.00 | 0.09 | 0.00 | 0.03 | 0.00 | 0.00 | 0.05 | 0.06 |
| ARSF | ENSG00000062096 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.04 | 0.01 | 0.08 | 0.07 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.07 | 0.11 | 0.07 | 0.03 | 0.03 | 0.07 | 0.12 | 0.07 | 0.04 | 0.02 | 0.02 | 0.07 | 0.08 | 0.00 | 0.00 | 0.02 | 0.04 | 0.02 | 0.01 | 0.11 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.06 | 0.05 | 0.20 | 0.20 | 0.09 | 0.02 | 0.05 | 0.04 | 0.09 | 0.11 | 0.21 | 0.11 | 0.05 | 0.02 | 0.00 | 0.00 | 0.00 | 0.07 | 0.04 | 0.02 | 0.02 | 0.01 | 0.00 | 0.01 | 0.04 | 0.02 |
| POLD1 | ENSG00000062822 | 0.00 | 0.00 | 0.01 | 0.02 | 0.00 | 0.00 | 0.01 | 0.01 | 0.10 | 0.04 | 0.00 | 0.02 | 0.00 | 0.06 | 0.01 | 0.07 | 0.07 | 0.11 | 0.03 | 0.02 | 0.07 | 0.03 | 0.09 | 0.03 | 0.02 | 0.03 | 0.02 | 0.03 | 0.03 | 0.05 | 0.05 | 0.04 | 0.00 | 0.07 | 0.23 | 0.02 | 0.00 | 0.03 | 0.00 | 0.00 | 0.11 | 0.04 | 0.05 | 0.31 | 0.06 | 0.07 | 0.03 | 0.05 | 0.15 | 0.13 | 0.03 | 0.17 | 0.00 | 0.04 | 0.01 | 0.00 | 0.24 | 0.03 | 0.00 | 0.15 | 0.02 | 0.13 | 0.00 | 0.00 | 0.03 | 0.02 |
| SLC6A16 | ENSG00000063127 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.02 | 0.11 | 0.04 | 0.00 | 0.02 | 0.00 | 0.06 | 0.01 | 0.07 | 0.04 | 0.10 | 0.03 | 0.02 | 0.09 | 0.05 | 0.06 | 0.03 | 0.01 | 0.02 | 0.02 | 0.03 | 0.03 | 0.05 | 0.04 | 0.04 | 0.00 | 0.07 | 0.18 | 0.02 | 0.00 | 0.03 | 0.00 | 0.00 | 0.09 | 0.05 | 0.04 | 0.32 | 0.05 | 0.06 | 0.05 | 0.05 | 0.18 | 0.18 | 0.04 | 0.18 | 0.00 | 0.04 | 0.01 | 0.00 | 0.07 | 0.05 | 0.00 | 0.13 | 0.02 | 0.12 | 0.00 | 0.00 | 0.02 | 0.02 |
| SPHK2 | ENSG00000063176 | 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 | 0.06 | 0.01 | 0.08 | 0.04 | 0.10 | 0.02 | 0.02 | 0.07 | 0.05 | 0.06 | 0.03 | 0.01 | 0.02 | 0.01 | 0.03 | 0.03 | 0.05 | 0.03 | 0.04 | 0.00 | 0.07 | 0.19 | 0.02 | 0.01 | 0.03 | 0.00 | 0.00 | 0.06 | 0.05 | 0.05 | 0.33 | 0.06 | 0.07 | 0.03 | 0.06 | 0.18 | 0.22 | 0.02 | 0.17 | 0.00 | 0.04 | 0.01 | 0.00 | 0.07 | 0.03 | 0.00 | 0.13 | 0.01 | 0.14 | 0.00 | 0.00 | 0.02 | 0.03 |
| GPC1 | ENSG00000063660 | 0.01 | 0.08 | 0.04 | 0.05 | 0.00 | 0.10 | 0.01 | 0.04 | 0.00 | 0.33 | 0.00 | 0.02 | 0.00 | 0.05 | 0.04 | 0.05 | 0.03 | 0.19 | 0.02 | 0.18 | 0.03 | 0.16 | 0.03 | 0.10 | 0.03 | 0.04 | 0.04 | 0.04 | 0.04 | 0.04 | 0.03 | 0.09 | 0.10 | 0.01 | 0.05 | 0.12 | 0.00 | 0.01 | 0.00 | 0.01 | 0.03 | 0.11 | 0.20 | 0.29 | 0.03 | 0.38 | 0.03 | 0.06 | 0.13 | 0.09 | 0.10 | 0.48 | 0.03 | 0.06 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.14 | 0.00 | 0.04 | 0.01 | 0.08 | 0.01 | 0.16 |
| WISP2 | ENSG00000064205 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.23 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.05 | 0.07 | 0.01 | 0.02 | 0.02 | 0.16 | 0.00 | 0.20 | 0.00 | 0.20 | 0.00 | 0.14 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.00 | 0.04 | 0.04 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.11 | 0.02 | 0.20 | 0.05 | 0.02 | 0.04 | 0.08 | 0.01 | 0.42 | 0.00 | 0.11 | 0.03 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.05 | 0.01 |
| HIPK2 | ENSG00000064393 | 0.02 | 0.01 | 0.07 | 0.00 | 0.06 | 0.02 | 0.03 | 0.02 | 0.04 | 0.04 | 0.00 | 0.01 | 0.04 | 0.09 | 0.08 | 0.02 | 0.09 | 0.06 | 0.03 | 0.14 | 0.04 | 0.19 | 0.05 | 0.08 | 0.03 | 0.00 | 0.04 | 0.01 | 0.04 | 0.04 | 0.05 | 0.05 | 0.00 | 0.06 | 0.03 | 0.06 | 0.01 | 0.02 | 0.00 | 0.00 | 0.09 | 0.04 | 0.52 | 0.04 | 0.03 | 0.08 | 0.07 | 0.06 | 0.17 | 0.14 | 0.10 | 0.09 | 0.02 | 0.04 | 0.00 | 0.05 | 0.02 | 0.11 | 0.12 | 0.00 | 0.05 | 0.01 | 0.00 | 0.00 | 0.24 | 0.02 |
| LPAR2 | ENSG00000064547 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.05 | 0.03 | 0.01 | 0.03 | 0.05 | 0.00 | 0.04 | 0.03 | 0.12 | 0.02 | 0.04 | 0.02 | 0.17 | 0.02 | 0.04 | 0.01 | 0.00 | 0.00 | 0.02 | 0.04 | 0.01 | 0.02 | 0.07 | 0.02 | 0.00 | 0.03 | 0.16 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.08 | 0.02 | 0.41 | 0.07 | 0.02 | 0.02 | 0.13 | 0.04 | 0.22 | 0.09 | 0.06 | 0.04 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.06 | 0.01 | 0.00 | 0.01 | 0.01 | 0.02 | 0.00 | 0.04 | 0.01 |
| CTSA | ENSG00000064601 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.01 | 0.09 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.05 | 0.08 | 0.01 | 0.01 | 0.01 | 0.06 | 0.00 | 0.18 | 0.00 | 0.16 | 0.00 | 0.13 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.00 | 0.01 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.15 | 0.02 | 0.23 | 0.04 | 0.02 | 0.05 | 0.08 | 0.01 | 0.42 | 0.00 | 0.10 | 0.03 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.08 | 0.01 |
| OAT | ENSG00000065154 | 0.00 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.06 | 0.03 | 0.10 | 0.00 | 0.02 | 0.02 | 0.15 | 0.04 | 0.03 | 0.05 | 0.07 | 0.02 | 0.03 | 0.06 | 0.05 | 0.17 | 0.05 | 0.01 | 0.05 | 0.01 | 0.05 | 0.03 | 0.01 | 0.01 | 0.09 | 0.14 | 0.17 | 0.13 | 0.02 | 0.01 | 0.02 | 0.00 | 0.00 | 0.08 | 0.09 | 0.26 | 0.19 | 0.02 | 0.05 | 0.06 | 0.06 | 0.07 | 0.04 | 0.07 | 0.08 | 0.09 | 0.01 | 0.00 | 0.00 | 0.00 | 0.05 | 0.01 | 0.13 | 0.00 | 0.07 | 0.00 | 0.00 | 0.01 | 0.04 |
| KARS | ENSG00000065427 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.06 | 0.00 | 0.21 | 0.12 | 0.02 | 0.00 | 0.00 | 0.00 | 0.10 | 0.05 | 0.05 | 0.06 | 0.04 | 0.03 | 0.02 | 0.06 | 0.04 | 0.04 | 0.04 | 0.01 | 0.00 | 0.02 | 0.02 | 0.01 | 0.01 | 0.00 | 0.05 | 0.05 | 0.01 | 0.05 | 0.09 | 0.00 | 0.00 | 0.00 | 0.01 | 0.04 | 0.06 | 0.07 | 0.28 | 0.04 | 0.02 | 0.03 | 0.08 | 0.01 | 0.19 | 0.02 | 0.05 | 0.01 | 0.08 | 0.00 | 0.05 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.05 | 0.00 | 0.00 | 0.02 | 0.04 |
| PRKCQ | ENSG00000065675 | 0.02 | 0.01 | 0.03 | 0.00 | 0.00 | 0.00 | 0.02 | 0.03 | 0.39 | 0.01 | 0.00 | 0.00 | 0.02 | 0.13 | 0.04 | 0.05 | 0.03 | 0.07 | 0.02 | 0.04 | 0.08 | 0.05 | 0.06 | 0.04 | 0.01 | 0.02 | 0.02 | 0.00 | 0.03 | 0.03 | 0.02 | 0.02 | 0.00 | 0.05 | 0.05 | 0.03 | 0.01 | 0.00 | 0.00 | 0.00 | 0.17 | 0.01 | 0.29 | 0.11 | 0.03 | 0.02 | 0.04 | 0.01 | 0.26 | 0.00 | 0.06 | 0.11 | 0.00 | 0.03 | 0.00 | 0.00 | 0.04 | 0.02 | 0.04 | 0.00 | 0.03 | 0.01 | 0.00 | 0.02 | 0.02 | 0.02 |
| SLC9A7 | ENSG00000065923 | 0.01 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.03 | 0.00 | 0.06 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.10 | 0.02 | 0.08 | 0.03 | 0.05 | 0.02 | 0.04 | 0.04 | 0.05 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.02 | 0.01 | 0.00 | 0.01 | 0.16 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.07 | 0.01 | 0.36 | 0.08 | 0.03 | 0.03 | 0.15 | 0.01 | 0.43 | 0.04 | 0.12 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.07 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.04 | 0.00 |
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