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 |
| CDYL | ENSG00000153046 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.06 | 0.20 | 0.09 | 0.00 | 0.05 | 0.03 | 0.01 | 0.10 | 0.02 | 0.09 | 0.08 | 0.05 | 0.06 | 0.08 | 0.24 | 0.04 | 0.11 | 0.02 | 0.03 | 0.02 | 0.05 | 0.00 | 0.07 | 0.15 | 0.02 | 0.06 | 0.03 | 0.11 | 0.05 | 0.00 | 0.01 | 0.00 | 0.00 | 0.12 | 0.07 | 0.45 | 0.11 | 0.10 | 0.06 | 0.09 | 0.03 | 0.21 | 0.05 | 0.11 | 0.13 | 0.04 | 0.03 | 0.00 | 0.00 | 0.10 | 0.01 | 0.02 | 0.03 | 0.02 | 0.03 | 0.28 | 0.00 | 0.24 | 0.00 |
| CLCN5 | ENSG00000171365 | 0.01 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.07 | 0.02 | 0.06 | 0.02 | 0.02 | 0.04 | 0.07 | 0.06 | 0.04 | 0.02 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.01 | 0.17 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.05 | 0.01 | 0.45 | 0.06 | 0.06 | 0.03 | 0.11 | 0.02 | 0.19 | 0.03 | 0.13 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.07 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.01 | 0.01 |
| CDKL2 | ENSG00000138769 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.03 | 0.01 | 0.13 | 0.02 | 0.00 | 0.00 | 0.00 | 0.08 | 0.07 | 0.03 | 0.22 | 0.01 | 0.09 | 0.01 | 0.18 | 0.03 | 0.10 | 0.04 | 0.01 | 0.02 | 0.03 | 0.01 | 0.01 | 0.01 | 0.02 | 0.08 | 0.05 | 0.03 | 0.08 | 0.00 | 0.02 | 0.02 | 0.00 | 0.00 | 0.14 | 0.02 | 0.24 | 0.12 | 0.07 | 0.02 | 0.04 | 0.01 | 0.05 | 0.05 | 0.08 | 0.06 | 0.06 | 0.01 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.01 |
| KCNJ3 | ENSG00000162989 | 0.01 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.08 | 0.03 | 0.04 | 0.00 | 0.01 | 0.00 | 0.01 | 0.04 | 0.02 | 0.06 | 0.03 | 0.03 | 0.01 | 0.08 | 0.03 | 0.02 | 0.04 | 0.00 | 0.02 | 0.00 | 0.01 | 0.02 | 0.02 | 0.04 | 0.07 | 0.00 | 0.05 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.04 | 0.26 | 0.05 | 0.04 | 0.02 | 0.04 | 0.01 | 0.01 | 0.00 | 0.07 | 0.06 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.14 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 |
| CACHD1 | ENSG00000158966 | 0.00 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.10 | 0.07 | 0.06 | 0.00 | 0.02 | 0.04 | 0.01 | 0.06 | 0.05 | 0.06 | 0.06 | 0.04 | 0.04 | 0.06 | 0.06 | 0.02 | 0.04 | 0.00 | 0.07 | 0.00 | 0.06 | 0.00 | 0.01 | 0.04 | 0.04 | 0.00 | 0.13 | 0.02 | 0.03 | 0.01 | 0.18 | 0.00 | 0.00 | 0.07 | 0.07 | 0.22 | 0.13 | 0.05 | 0.03 | 0.03 | 0.02 | 0.00 | 0.06 | 0.25 | 0.02 | 0.03 | 0.05 | 0.02 | 0.01 | 0.00 | 0.03 | 0.00 | 0.01 | 0.02 | 0.01 | 0.00 | 0.07 | 0.04 | 0.04 |
| HABP2 | ENSG00000148702 | 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 | 0.07 | 0.03 | 0.04 | 0.06 | 0.01 | 0.03 | 0.04 | 0.06 | 0.08 | 0.06 | 0.01 | 0.07 | 0.01 | 0.07 | 0.01 | 0.01 | 0.04 | 0.10 | 0.11 | 0.21 | 0.11 | 0.00 | 0.01 | 0.02 | 0.00 | 0.00 | 0.03 | 0.10 | 0.19 | 0.22 | 0.01 | 0.08 | 0.03 | 0.07 | 0.07 | 0.05 | 0.04 | 0.04 | 0.07 | 0.00 | 0.00 | 0.00 | 0.00 | 0.10 | 0.00 | 0.11 | 0.01 | 0.06 | 0.00 | 0.00 | 0.01 | 0.05 |
| A2ML1 | ENSG00000166535 | 0.01 | 0.01 | 0.00 | 0.01 | 0.02 | 0.00 | 0.01 | 0.10 | 0.07 | 0.03 | 0.01 | 0.00 | 0.00 | 0.07 | 0.05 | 0.08 | 0.13 | 0.01 | 0.11 | 0.02 | 0.07 | 0.02 | 0.08 | 0.08 | 0.02 | 0.02 | 0.04 | 0.04 | 0.00 | 0.07 | 0.02 | 0.05 | 0.14 | 0.05 | 0.03 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.09 | 0.04 | 0.32 | 0.09 | 0.03 | 0.02 | 0.03 | 0.03 | 0.02 | 0.03 | 0.11 | 0.11 | 0.57 | 0.00 | 0.00 | 0.01 | 0.00 | 0.08 | 0.11 | 0.01 | 0.03 | 0.04 | 0.00 | 0.01 | 0.05 | 0.04 |
| DUSP16 | ENSG00000111266 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.19 | 0.03 | 0.07 | 0.01 | 0.00 | 0.00 | 0.06 | 0.03 | 0.09 | 0.09 | 0.02 | 0.08 | 0.03 | 0.06 | 0.03 | 0.06 | 0.08 | 0.01 | 0.04 | 0.00 | 0.08 | 0.03 | 0.05 | 0.02 | 0.06 | 0.14 | 0.05 | 0.03 | 0.00 | 0.00 | 0.01 | 0.00 | 0.01 | 0.06 | 0.08 | 0.26 | 0.11 | 0.01 | 0.03 | 0.04 | 0.03 | 0.08 | 0.03 | 0.11 | 0.17 | 0.54 | 0.00 | 0.00 | 0.06 | 0.00 | 0.13 | 0.04 | 0.03 | 0.01 | 0.07 | 0.00 | 0.01 | 0.04 | 0.03 |
| ITPKC | ENSG00000086544 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.02 | 0.01 | 0.03 | 0.19 | 0.02 | 0.00 | 0.00 | 0.08 | 0.02 | 0.13 | 0.03 | 0.33 | 0.06 | 0.04 | 0.02 | 0.03 | 0.05 | 0.08 | 0.03 | 0.05 | 0.01 | 0.01 | 0.02 | 0.14 | 0.02 | 0.08 | 0.02 | 0.12 | 0.01 | 0.09 | 0.04 | 0.00 | 0.02 | 0.00 | 0.00 | 0.09 | 0.04 | 0.36 | 0.24 | 0.10 | 0.04 | 0.10 | 0.04 | 0.88 | 0.11 | 0.22 | 0.12 | 0.00 | 0.03 | 0.01 | 0.00 | 0.05 | 0.00 | 0.02 | 0.07 | 0.02 | 0.07 | 0.00 | 0.00 | 0.02 | 0.02 |
| CRLF1 | ENSG00000006016 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.03 | 0.01 | 0.04 | 0.07 | 0.01 | 0.03 | 0.03 | 0.11 | 0.02 | 0.05 | 0.02 | 0.14 | 0.01 | 0.03 | 0.02 | 0.00 | 0.00 | 0.01 | 0.04 | 0.02 | 0.02 | 0.08 | 0.02 | 0.06 | 0.03 | 0.21 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.09 | 0.02 | 0.52 | 0.05 | 0.02 | 0.02 | 0.19 | 0.04 | 0.45 | 0.07 | 0.07 | 0.03 | 0.01 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.02 | 0.00 | 0.02 | 0.01 | 0.02 | 0.00 | 0.03 | 0.01 |
| ITGAM | ENSG00000169896 | 0.00 | 0.00 | 0.03 | 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 | 0.01 | 0.04 | 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 | 0.10 | 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 |
| PTPN6 | ENSG00000111679 | 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 | 0.18 | 0.01 | 0.11 | 0.01 | 0.08 | 0.02 | 0.06 | 0.05 | 0.06 | 0.02 | 0.04 | 0.02 | 0.06 | 0.05 | 0.04 | 0.04 | 0.18 | 0.05 | 0.09 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.13 | 0.04 | 0.35 | 0.07 | 0.04 | 0.02 | 0.09 | 0.02 | 0.17 | 0.03 | 0.08 | 0.11 | 0.60 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.14 | 0.01 | 0.05 | 0.01 | 0.00 | 0.01 | 0.04 | 0.04 |
| NEK8 | ENSG00000160602 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.01 | 0.28 | 0.01 | 0.08 | 0.00 | 0.00 | 0.03 | 0.08 | 0.01 | 0.10 | 0.04 | 0.05 | 0.02 | 0.14 | 0.02 | 0.11 | 0.01 | 0.10 | 0.01 | 0.07 | 0.01 | 0.03 | 0.01 | 0.06 | 0.00 | 0.07 | 0.01 | 0.04 | 0.04 | 0.00 | 0.14 | 0.00 | 0.00 | 0.37 | 0.03 | 0.20 | 0.07 | 0.02 | 0.03 | 0.19 | 0.01 | 0.21 | 0.05 | 0.03 | 0.16 | 0.00 | 0.01 | 0.00 | 0.02 | 0.04 | 0.00 | 0.00 | 0.01 | 0.01 | 0.03 | 0.00 | 0.00 | 0.04 | 0.03 |
| SLC22A9 | ENSG00000149742 | 0.01 | 0.00 | 0.00 | 0.01 | 0.07 | 0.00 | 0.02 | 0.01 | 0.11 | 0.01 | 0.00 | 0.00 | 0.12 | 0.01 | 0.05 | 0.02 | 0.08 | 0.01 | 0.16 | 0.03 | 0.11 | 0.04 | 0.04 | 0.02 | 0.01 | 0.02 | 0.03 | 0.03 | 0.00 | 0.03 | 0.02 | 0.03 | 0.09 | 0.07 | 0.05 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.09 | 0.07 | 0.14 | 0.04 | 0.07 | 0.01 | 0.07 | 0.02 | 0.47 | 0.12 | 0.08 | 0.03 | 0.00 | 0.06 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.05 | 0.04 |
| IL17RE | ENSG00000163701 | 0.00 | 0.18 | 0.00 | 0.01 | 0.07 | 0.00 | 0.01 | 0.06 | 0.42 | 0.02 | 0.00 | 0.03 | 0.03 | 0.06 | 0.05 | 0.04 | 0.02 | 0.04 | 0.03 | 0.02 | 0.08 | 0.05 | 0.07 | 0.06 | 0.00 | 0.04 | 0.01 | 0.06 | 0.01 | 0.02 | 0.08 | 0.01 | 0.00 | 0.18 | 0.13 | 0.01 | 0.00 | 0.04 | 0.00 | 0.00 | 0.13 | 0.02 | 0.17 | 0.22 | 0.02 | 0.02 | 0.05 | 0.03 | 0.11 | 0.14 | 0.23 | 0.05 | 0.05 | 0.05 | 0.00 | 0.00 | 0.00 | 0.05 | 0.04 | 0.01 | 0.03 | 0.01 | 0.00 | 0.00 | 0.02 | 0.05 |
| IGFBP2 | ENSG00000115457 | 0.01 | 0.07 | 0.04 | 0.03 | 0.00 | 0.03 | 0.01 | 0.02 | 0.01 | 0.26 | 0.00 | 0.00 | 0.00 | 0.12 | 0.02 | 0.03 | 0.04 | 0.19 | 0.00 | 0.18 | 0.03 | 0.11 | 0.05 | 0.03 | 0.02 | 0.02 | 0.02 | 0.02 | 0.06 | 0.03 | 0.04 | 0.04 | 0.00 | 0.01 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.04 | 0.05 | 0.20 | 0.16 | 0.03 | 0.34 | 0.04 | 0.03 | 0.15 | 0.05 | 0.06 | 0.22 | 0.08 | 0.01 | 0.00 | 0.00 | 0.00 | 0.04 | 0.00 | 0.02 | 0.01 | 0.00 | 0.02 | 0.02 | 0.02 | 0.03 |
| BBOX1 | ENSG00000129151 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.05 | 0.05 | 0.00 | 0.00 | 0.00 | 0.04 | 0.06 | 0.02 | 0.05 | 0.05 | 0.03 | 0.03 | 0.20 | 0.02 | 0.05 | 0.02 | 0.02 | 0.01 | 0.00 | 0.02 | 0.01 | 0.02 | 0.04 | 0.01 | 0.00 | 0.01 | 0.02 | 0.01 | 0.02 | 0.07 | 0.00 | 0.00 | 0.07 | 0.04 | 0.12 | 0.13 | 0.00 | 0.05 | 0.05 | 0.03 | 0.01 | 0.10 | 0.04 | 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 |
| PKHD1 | ENSG00000170927 | 0.00 | 0.00 | 0.04 | 0.02 | 0.00 | 0.00 | 0.01 | 0.02 | 0.10 | 0.04 | 0.00 | 0.00 | 0.00 | 0.02 | 0.07 | 0.01 | 0.22 | 0.04 | 0.09 | 0.02 | 0.32 | 0.03 | 0.14 | 0.01 | 0.02 | 0.01 | 0.11 | 0.02 | 0.01 | 0.01 | 0.09 | 0.00 | 0.00 | 0.01 | 0.09 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.11 | 0.02 | 0.17 | 0.06 | 0.09 | 0.03 | 0.05 | 0.01 | 0.17 | 0.03 | 0.14 | 0.03 | 0.02 | 0.00 | 0.00 | 0.00 | 0.09 | 0.03 | 0.01 | 0.00 | 0.00 | 0.03 | 0.01 | 0.00 | 0.04 | 0.02 |
| NCOA1 | ENSG00000084676 | 0.00 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 | 0.10 | 0.01 | 0.00 | 0.00 | 0.03 | 0.08 | 0.05 | 0.01 | 0.09 | 0.02 | 0.03 | 0.02 | 0.06 | 0.06 | 0.03 | 0.04 | 0.01 | 0.01 | 0.01 | 0.02 | 0.01 | 0.04 | 0.09 | 0.01 | 0.00 | 0.05 | 0.03 | 0.04 | 0.01 | 0.00 | 0.00 | 0.00 | 0.05 | 0.04 | 0.19 | 0.12 | 0.08 | 0.00 | 0.10 | 0.02 | 0.33 | 0.03 | 0.05 | 0.11 | 0.17 | 0.01 | 0.00 | 0.01 | 0.02 | 0.03 | 0.01 | 0.01 | 0.02 | 0.04 | 0.05 | 0.00 | 0.05 | 0.04 |
| ACRBP | ENSG00000111644 | 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 | 0.06 | 0.07 | 0.17 | 0.01 | 0.11 | 0.01 | 0.08 | 0.04 | 0.06 | 0.05 | 0.05 | 0.02 | 0.05 | 0.02 | 0.05 | 0.05 | 0.03 | 0.04 | 0.14 | 0.05 | 0.06 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.13 | 0.04 | 0.35 | 0.07 | 0.04 | 0.02 | 0.10 | 0.02 | 0.08 | 0.03 | 0.12 | 0.12 | 0.60 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.15 | 0.01 | 0.05 | 0.01 | 0.00 | 0.01 | 0.05 | 0.04 |
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