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 |
| IGFBP6 | ENSG00000167779 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.02 | 0.00 | 0.04 | 0.03 | 0.00 | 0.00 | 0.00 | 0.04 | 0.06 | 0.01 | 0.03 | 0.02 | 0.01 | 0.03 | 0.04 | 0.03 | 0.05 | 0.04 | 0.02 | 0.00 | 0.03 | 0.01 | 0.00 | 0.03 | 0.02 | 0.01 | 0.09 | 0.01 | 0.16 | 0.01 | 0.03 | 0.01 | 0.00 | 0.00 | 0.03 | 0.05 | 0.10 | 0.05 | 0.03 | 0.00 | 0.09 | 0.01 | 0.38 | 0.05 | 0.01 | 0.10 | 0.01 | 0.00 | 0.00 | 0.00 | 0.12 | 0.00 | 0.00 | 0.03 | 0.03 | 0.05 | 0.00 | 0.00 | 0.02 | 0.06 |
| ST3GAL3 | ENSG00000126091 | 0.00 | 0.02 | 0.01 | 0.03 | 0.00 | 0.00 | 0.01 | 0.02 | 0.14 | 0.03 | 0.00 | 0.00 | 0.08 | 0.03 | 0.09 | 0.02 | 0.12 | 0.02 | 0.08 | 0.01 | 0.11 | 0.04 | 0.04 | 0.03 | 0.02 | 0.02 | 0.02 | 0.01 | 0.03 | 0.00 | 0.02 | 0.08 | 0.00 | 0.27 | 0.02 | 0.03 | 0.03 | 0.11 | 0.00 | 0.00 | 0.08 | 0.04 | 0.52 | 0.06 | 0.11 | 0.01 | 0.11 | 0.01 | 0.20 | 0.05 | 0.12 | 0.03 | 0.05 | 0.03 | 0.02 | 0.00 | 0.00 | 0.05 | 0.00 | 0.01 | 0.03 | 0.00 | 0.00 | 0.07 | 0.04 | 0.02 |
| GRK4 | ENSG00000125388 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.03 | 0.02 | 0.08 | 0.04 | 0.00 | 0.00 | 0.00 | 0.03 | 0.04 | 0.04 | 0.04 | 0.04 | 0.03 | 0.06 | 0.07 | 0.09 | 0.05 | 0.06 | 0.02 | 0.03 | 0.04 | 0.03 | 0.01 | 0.02 | 0.05 | 0.06 | 0.00 | 0.01 | 0.09 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.03 | 0.06 | 0.33 | 0.07 | 0.02 | 0.05 | 0.08 | 0.05 | 0.10 | 0.00 | 0.12 | 0.04 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.00 | 0.01 | 0.02 | 0.02 | 0.00 | 0.03 | 0.05 |
| CYP3A5 | ENSG00000106258 | 0.01 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.05 | 0.02 | 0.08 | 0.01 | 0.00 | 0.00 | 0.03 | 0.00 | 0.12 | 0.01 | 0.24 | 0.01 | 0.24 | 0.00 | 0.56 | 0.02 | 0.31 | 0.01 | 0.02 | 0.00 | 0.02 | 0.00 | 0.11 | 0.01 | 0.08 | 0.01 | 0.11 | 0.01 | 0.10 | 0.03 | 0.00 | 0.02 | 0.00 | 0.00 | 0.07 | 0.03 | 0.20 | 0.05 | 0.07 | 0.01 | 0.06 | 0.01 | 0.12 | 0.04 | 0.07 | 0.04 | 0.09 | 0.01 | 0.00 | 0.00 | 0.13 | 0.00 | 0.06 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.05 | 0.03 |
| CACNA1I | ENSG00000100346 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.04 | 0.07 | 0.00 | 0.04 | 0.00 | 0.02 | 0.04 | 0.04 | 0.08 | 0.02 | 0.03 | 0.01 | 0.01 | 0.00 | 0.01 | 0.02 | 0.01 | 0.02 | 0.01 | 0.02 | 0.02 | 0.02 | 0.04 | 0.02 | 0.00 | 0.01 | 0.02 | 0.05 | 0.00 | 0.05 | 0.00 | 0.00 | 0.02 | 0.02 | 0.09 | 0.15 | 0.03 | 0.03 | 0.09 | 0.02 | 0.14 | 0.15 | 0.09 | 0.03 | 0.01 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.04 | 0.02 | 0.00 | 0.18 | 0.00 |
| STK36 | ENSG00000163482 | 0.01 | 0.07 | 0.04 | 0.04 | 0.00 | 0.03 | 0.01 | 0.02 | 0.01 | 0.27 | 0.00 | 0.01 | 0.00 | 0.10 | 0.02 | 0.03 | 0.04 | 0.19 | 0.01 | 0.18 | 0.03 | 0.11 | 0.06 | 0.04 | 0.02 | 0.01 | 0.02 | 0.02 | 0.05 | 0.03 | 0.03 | 0.04 | 0.00 | 0.01 | 0.04 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.04 | 0.06 | 0.17 | 0.16 | 0.04 | 0.35 | 0.06 | 0.04 | 0.22 | 0.05 | 0.08 | 0.21 | 0.08 | 0.01 | 0.00 | 0.00 | 0.00 | 0.04 | 0.01 | 0.02 | 0.01 | 0.00 | 0.02 | 0.02 | 0.03 | 0.03 |
| SFTPB | ENSG00000168878 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.02 | 0.02 | 0.09 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.03 | 0.01 | 0.12 | 0.01 | 0.08 | 0.01 | 0.11 | 0.01 | 0.05 | 0.01 | 0.00 | 0.01 | 0.01 | 0.01 | 0.01 | 0.01 | 0.04 | 0.02 | 0.00 | 0.02 | 0.04 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.05 | 0.02 | 0.12 | 0.04 | 0.05 | 0.00 | 0.09 | 0.01 | 0.19 | 0.03 | 0.26 | 0.03 | 0.03 | 0.04 | 0.00 | 0.00 | 0.04 | 0.04 | 0.00 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 |
| BPIFB1 | ENSG00000125999 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.02 | 0.01 | 0.21 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.07 | 0.02 | 0.21 | 0.00 | 0.19 | 0.00 | 0.09 | 0.00 | 0.05 | 0.01 | 0.11 | 0.00 | 0.17 | 0.00 | 0.02 | 0.01 | 0.02 | 0.00 | 0.00 | 0.01 | 0.05 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.02 | 0.20 | 0.02 | 0.19 | 0.00 | 0.09 | 0.01 | 0.43 | 0.00 | 0.09 | 0.02 | 0.03 | 0.00 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.05 | 0.00 |
| RARB | ENSG00000077092 | 0.00 | 0.18 | 0.00 | 0.01 | 0.07 | 0.00 | 0.00 | 0.03 | 0.19 | 0.02 | 0.00 | 0.03 | 0.02 | 0.07 | 0.02 | 0.05 | 0.01 | 0.05 | 0.00 | 0.03 | 0.05 | 0.06 | 0.04 | 0.06 | 0.00 | 0.02 | 0.03 | 0.02 | 0.02 | 0.02 | 0.07 | 0.02 | 0.00 | 0.11 | 0.05 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.07 | 0.05 | 0.13 | 0.18 | 0.01 | 0.04 | 0.05 | 0.03 | 0.12 | 0.11 | 0.14 | 0.01 | 0.05 | 0.04 | 0.00 | 0.01 | 0.04 | 0.01 | 0.02 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.03 | 0.04 |
| CDK19 | ENSG00000155111 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.30 | 0.03 | 0.12 | 0.00 | 0.01 | 0.00 | 0.14 | 0.02 | 0.06 | 0.03 | 0.05 | 0.02 | 0.03 | 0.04 | 0.08 | 0.05 | 0.07 | 0.01 | 0.03 | 0.01 | 0.04 | 0.00 | 0.03 | 0.01 | 0.08 | 0.00 | 0.15 | 0.05 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.12 | 0.09 | 0.08 | 0.26 | 0.02 | 0.02 | 0.09 | 0.02 | 0.15 | 0.04 | 0.23 | 0.08 | 0.00 | 0.04 | 0.00 | 0.00 | 0.01 | 0.21 | 0.00 | 0.02 | 0.02 | 0.06 | 0.04 | 0.03 | 0.00 | 0.13 |
| TNFRSF13B | ENSG00000240505 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.03 | 0.04 | 0.09 | 0.00 | 0.01 | 0.02 | 0.03 | 0.03 | 0.03 | 0.02 | 0.03 | 0.05 | 0.02 | 0.05 | 0.07 | 0.02 | 0.04 | 0.00 | 0.03 | 0.00 | 0.03 | 0.01 | 0.00 | 0.03 | 0.04 | 0.06 | 0.05 | 0.02 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.07 | 0.05 | 0.01 | 0.14 | 0.02 | 0.05 | 0.04 | 0.06 | 0.15 | 0.16 | 0.69 | 0.02 | 0.07 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.02 |
| LRRC4C | ENSG00000148948 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.03 | 0.01 | 0.08 | 0.06 | 0.07 | 0.00 | 0.00 | 0.04 | 0.04 | 0.05 | 0.02 | 0.09 | 0.04 | 0.09 | 0.02 | 0.17 | 0.04 | 0.07 | 0.02 | 0.01 | 0.01 | 0.02 | 0.03 | 0.03 | 0.02 | 0.01 | 0.01 | 0.00 | 0.07 | 0.06 | 0.08 | 0.01 | 0.09 | 0.00 | 0.00 | 0.09 | 0.04 | 0.12 | 0.09 | 0.11 | 0.03 | 0.03 | 0.02 | 0.04 | 0.16 | 0.09 | 0.11 | 0.00 | 0.06 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.04 | 0.00 | 0.06 | 0.00 | 0.02 | 0.02 | 0.05 |
| UHRF2 | ENSG00000147854 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.06 | 0.15 | 0.13 | 0.01 | 0.01 | 0.04 | 0.06 | 0.05 | 0.14 | 0.14 | 0.11 | 0.22 | 0.06 | 0.13 | 0.13 | 0.09 | 0.11 | 0.01 | 0.03 | 0.05 | 0.04 | 0.00 | 0.10 | 0.05 | 0.03 | 0.03 | 0.01 | 0.02 | 0.03 | 0.01 | 0.03 | 0.00 | 0.00 | 0.10 | 0.06 | 0.16 | 0.19 | 0.21 | 0.04 | 0.06 | 0.03 | 0.02 | 0.17 | 0.24 | 0.13 | 0.01 | 0.09 | 0.00 | 0.00 | 0.04 | 0.02 | 0.00 | 0.10 | 0.01 | 0.20 | 0.00 | 0.00 | 0.04 | 0.12 |
| L3MBTL3 | ENSG00000198945 | 0.00 | 0.05 | 0.00 | 0.00 | 0.00 | 0.05 | 0.01 | 0.01 | 0.07 | 0.05 | 0.00 | 0.01 | 0.00 | 0.13 | 0.02 | 0.05 | 0.06 | 0.05 | 0.04 | 0.02 | 0.14 | 0.01 | 0.06 | 0.04 | 0.03 | 0.01 | 0.04 | 0.03 | 0.00 | 0.02 | 0.01 | 0.09 | 0.00 | 0.16 | 0.03 | 0.04 | 0.00 | 0.01 | 0.00 | 0.00 | 0.11 | 0.04 | 0.10 | 0.27 | 0.01 | 0.02 | 0.04 | 0.03 | 0.08 | 0.03 | 0.24 | 0.05 | 0.01 | 0.03 | 0.00 | 0.00 | 0.00 | 0.15 | 0.00 | 0.05 | 0.00 | 0.10 | 0.04 | 0.06 | 0.01 | 0.13 |
| EFEMP2 | ENSG00000172638 | 0.01 | 0.00 | 0.00 | 0.01 | 0.07 | 0.00 | 0.08 | 0.01 | 0.20 | 0.01 | 0.00 | 0.00 | 0.08 | 0.00 | 0.09 | 0.03 | 0.09 | 0.02 | 0.30 | 0.02 | 0.18 | 0.04 | 0.07 | 0.03 | 0.01 | 0.02 | 0.02 | 0.04 | 0.00 | 0.03 | 0.02 | 0.04 | 0.00 | 0.11 | 0.07 | 0.07 | 0.03 | 0.01 | 0.00 | 0.00 | 0.14 | 0.09 | 0.23 | 0.04 | 0.13 | 0.01 | 0.07 | 0.03 | 0.20 | 0.06 | 0.13 | 0.03 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.01 | 0.01 | 0.03 | 0.00 | 0.00 | 0.08 | 0.06 |
| HTRA1 | ENSG00000166033 | 0.00 | 0.02 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.05 | 0.05 | 0.10 | 0.00 | 0.02 | 0.02 | 0.16 | 0.03 | 0.03 | 0.05 | 0.06 | 0.01 | 0.03 | 0.11 | 0.05 | 0.15 | 0.05 | 0.01 | 0.05 | 0.01 | 0.04 | 0.02 | 0.01 | 0.03 | 0.12 | 0.20 | 0.11 | 0.11 | 0.02 | 0.01 | 0.02 | 0.00 | 0.00 | 0.08 | 0.10 | 0.22 | 0.21 | 0.02 | 0.06 | 0.06 | 0.06 | 0.09 | 0.04 | 0.05 | 0.08 | 0.10 | 0.03 | 0.00 | 0.00 | 0.00 | 0.05 | 0.01 | 0.13 | 0.00 | 0.07 | 0.00 | 0.00 | 0.01 | 0.04 |
| KDM3B | ENSG00000120733 | 0.29 | 0.00 | 0.03 | 0.01 | 0.00 | 0.00 | 0.02 | 0.03 | 0.03 | 0.03 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.04 | 0.03 | 0.03 | 0.01 | 0.03 | 0.03 | 0.03 | 0.02 | 0.05 | 0.01 | 0.02 | 0.02 | 0.02 | 0.01 | 0.01 | 0.10 | 0.02 | 0.09 | 0.01 | 0.24 | 0.02 | 0.02 | 0.06 | 0.01 | 0.00 | 0.04 | 0.02 | 0.13 | 0.12 | 0.03 | 0.01 | 0.03 | 0.01 | 0.15 | 0.01 | 0.08 | 0.04 | 0.00 | 0.00 | 0.00 | 0.10 | 0.04 | 0.00 | 0.01 | 0.04 | 0.01 | 0.02 | 0.00 | 0.03 | 0.04 | 0.13 |
| KCNB1 | ENSG00000158445 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.01 | 0.10 | 0.01 | 0.00 | 0.00 | 0.03 | 0.00 | 0.10 | 0.03 | 0.08 | 0.01 | 0.01 | 0.01 | 0.10 | 0.01 | 0.22 | 0.00 | 0.13 | 0.00 | 0.13 | 0.00 | 0.01 | 0.00 | 0.07 | 0.01 | 0.00 | 0.01 | 0.08 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.24 | 0.01 | 0.26 | 0.02 | 0.02 | 0.03 | 0.09 | 0.01 | 0.40 | 0.00 | 0.15 | 0.03 | 0.01 | 0.00 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.12 | 0.00 |
| TRPM7 | ENSG00000092439 | 0.00 | 0.00 | 0.00 | 0.01 | 0.14 | 0.00 | 0.01 | 0.04 | 0.06 | 0.03 | 0.00 | 0.00 | 0.07 | 0.11 | 0.01 | 0.04 | 0.03 | 0.06 | 0.03 | 0.03 | 0.03 | 0.02 | 0.02 | 0.06 | 0.01 | 0.03 | 0.00 | 0.05 | 0.01 | 0.02 | 0.01 | 0.03 | 0.00 | 0.01 | 0.04 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.08 | 0.06 | 0.20 | 0.01 | 0.09 | 0.01 | 0.07 | 0.08 | 0.26 | 0.10 | 0.04 | 0.01 | 0.03 | 0.00 | 0.00 | 0.06 | 0.05 | 0.00 | 0.02 | 0.00 | 0.08 | 0.00 | 0.00 | 0.04 | 0.10 |
| CTSD | ENSG00000117984 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.04 | 0.01 | 0.02 | 0.01 | 0.12 | 0.00 | 0.00 | 0.02 | 0.05 | 0.03 | 0.07 | 0.01 | 0.16 | 0.02 | 0.07 | 0.04 | 0.14 | 0.02 | 0.06 | 0.03 | 0.02 | 0.01 | 0.03 | 0.01 | 0.06 | 0.04 | 0.03 | 0.03 | 0.01 | 0.08 | 0.14 | 0.02 | 0.06 | 0.00 | 0.00 | 0.02 | 0.12 | 0.05 | 0.48 | 0.01 | 0.07 | 0.04 | 0.08 | 0.05 | 0.09 | 0.07 | 0.16 | 0.02 | 0.05 | 0.00 | 0.00 | 0.05 | 0.00 | 0.01 | 0.11 | 0.01 | 0.06 | 0.00 | 0.00 | 0.02 | 0.05 |
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