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 |
| SMYD2 | ENSG00000143499 | 0.01 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.06 | 0.06 | 0.06 | 0.01 | 0.00 | 0.05 | 0.04 | 0.08 | 0.02 | 0.09 | 0.02 | 0.05 | 0.01 | 0.16 | 0.04 | 0.05 | 0.01 | 0.05 | 0.00 | 0.07 | 0.03 | 0.00 | 0.00 | 0.16 | 0.02 | 0.16 | 0.02 | 0.03 | 0.04 | 0.02 | 0.01 | 0.00 | 0.00 | 0.20 | 0.02 | 0.17 | 0.17 | 0.06 | 0.01 | 0.06 | 0.03 | 0.23 | 0.04 | 0.02 | 0.21 | 0.03 | 0.03 | 0.01 | 0.00 | 0.15 | 0.04 | 0.00 | 0.02 | 0.01 | 0.06 | 0.09 | 0.00 | 0.11 | 0.03 |
| SLC4A8 | ENSG00000050438 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.11 | 0.03 | 0.00 | 0.00 | 0.00 | 0.04 | 0.06 | 0.02 | 0.02 | 0.02 | 0.01 | 0.03 | 0.10 | 0.04 | 0.05 | 0.05 | 0.03 | 0.00 | 0.03 | 0.01 | 0.00 | 0.04 | 0.02 | 0.01 | 0.09 | 0.01 | 0.31 | 0.00 | 0.03 | 0.02 | 0.00 | 0.00 | 0.04 | 0.06 | 0.10 | 0.05 | 0.03 | 0.00 | 0.05 | 0.01 | 0.24 | 0.04 | 0.17 | 0.09 | 0.01 | 0.00 | 0.00 | 0.00 | 0.12 | 0.00 | 0.01 | 0.03 | 0.05 | 0.05 | 0.00 | 0.00 | 0.05 | 0.06 |
| MAPKAPK2 | ENSG00000162889 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.02 | 0.07 | 0.06 | 0.01 | 0.00 | 0.07 | 0.01 | 0.12 | 0.01 | 0.09 | 0.01 | 0.06 | 0.00 | 0.17 | 0.06 | 0.08 | 0.01 | 0.04 | 0.00 | 0.12 | 0.02 | 0.00 | 0.00 | 0.19 | 0.01 | 0.18 | 0.02 | 0.01 | 0.03 | 0.01 | 0.00 | 0.00 | 0.00 | 0.28 | 0.01 | 0.22 | 0.11 | 0.07 | 0.00 | 0.07 | 0.02 | 0.24 | 0.04 | 0.03 | 0.18 | 0.03 | 0.02 | 0.01 | 0.00 | 0.16 | 0.10 | 0.00 | 0.01 | 0.04 | 0.02 | 0.09 | 0.00 | 0.15 | 0.02 |
| STK4 | ENSG00000101109 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.21 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.05 | 0.07 | 0.01 | 0.02 | 0.02 | 0.13 | 0.00 | 0.21 | 0.00 | 0.19 | 0.00 | 0.14 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.00 | 0.04 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.13 | 0.03 | 0.24 | 0.05 | 0.03 | 0.05 | 0.11 | 0.01 | 0.39 | 0.00 | 0.11 | 0.03 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.01 |
| HSP90AB1 | ENSG00000096384 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.19 | 0.02 | 0.00 | 0.00 | 0.01 | 0.02 | 0.13 | 0.01 | 0.14 | 0.04 | 0.06 | 0.02 | 0.58 | 0.02 | 0.37 | 0.01 | 0.10 | 0.00 | 0.20 | 0.00 | 0.03 | 0.00 | 0.14 | 0.00 | 0.05 | 0.01 | 0.08 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.13 | 0.03 | 0.24 | 0.06 | 0.08 | 0.02 | 0.07 | 0.01 | 0.08 | 0.03 | 0.24 | 0.04 | 0.06 | 0.01 | 0.00 | 0.00 | 0.09 | 0.05 | 0.01 | 0.00 | 0.03 | 0.01 | 0.02 | 0.00 | 0.06 | 0.00 |
| HAO2 | ENSG00000116882 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.03 | 0.02 | 0.20 | 0.03 | 0.00 | 0.00 | 0.00 | 0.17 | 0.03 | 0.12 | 0.09 | 0.16 | 0.04 | 0.16 | 0.14 | 0.10 | 0.04 | 0.06 | 0.02 | 0.04 | 0.05 | 0.03 | 0.15 | 0.01 | 0.03 | 0.04 | 0.01 | 0.04 | 0.12 | 0.03 | 0.04 | 0.25 | 0.00 | 0.00 | 0.13 | 0.05 | 0.22 | 0.10 | 0.07 | 0.06 | 0.04 | 0.02 | 0.10 | 0.06 | 0.11 | 0.11 | 0.03 | 0.03 | 0.00 | 0.00 | 0.03 | 0.02 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.08 | 0.31 | 0.07 |
| PDPK1 | ENSG00000140992 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.01 | 0.15 | 0.00 | 0.00 | 0.04 | 0.02 | 0.04 | 0.03 | 0.03 | 0.08 | 0.03 | 0.03 | 0.03 | 0.09 | 0.02 | 0.08 | 0.03 | 0.03 | 0.03 | 0.02 | 0.01 | 0.02 | 0.03 | 0.02 | 0.00 | 0.05 | 0.17 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.09 | 0.02 | 0.11 | 0.16 | 0.10 | 0.03 | 0.06 | 0.03 | 0.03 | 0.05 | 0.10 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.09 | 0.00 | 0.01 | 0.00 | 0.03 | 0.01 | 0.00 | 0.00 | 0.05 | 0.02 |
| KLHL18 | ENSG00000114648 | 0.00 | 0.18 | 0.00 | 0.02 | 0.05 | 0.00 | 0.00 | 0.03 | 0.03 | 0.12 | 0.00 | 0.04 | 0.00 | 0.57 | 0.00 | 0.06 | 0.00 | 0.09 | 0.00 | 0.05 | 0.04 | 0.08 | 0.01 | 0.11 | 0.00 | 0.05 | 0.02 | 0.06 | 0.00 | 0.05 | 0.04 | 0.06 | 0.00 | 0.24 | 0.03 | 0.02 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.15 | 0.08 | 0.20 | 0.01 | 0.05 | 0.05 | 0.05 | 0.02 | 0.22 | 0.04 | 0.13 | 0.03 | 0.04 | 0.00 | 0.01 | 0.00 | 0.14 | 0.00 | 0.06 | 0.01 | 0.04 | 0.00 | 0.03 | 0.01 | 0.05 |
| DHRS12 | ENSG00000102796 | 0.00 | 0.02 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.35 | 0.03 | 0.25 | 0.00 | 0.00 | 0.00 | 0.14 | 0.03 | 0.06 | 0.02 | 0.10 | 0.01 | 0.11 | 0.09 | 0.07 | 0.12 | 0.03 | 0.10 | 0.02 | 0.11 | 0.04 | 0.01 | 0.01 | 0.02 | 0.27 | 0.00 | 0.09 | 0.00 | 0.06 | 0.00 | 0.00 | 0.00 | 0.02 | 0.02 | 0.12 | 0.05 | 0.22 | 0.02 | 0.20 | 0.00 | 0.03 | 0.03 | 0.12 | 0.01 | 0.35 | 0.03 | 0.02 | 0.00 | 0.00 | 0.03 | 0.06 | 0.00 | 0.09 | 0.00 | 0.16 | 0.00 | 0.00 | 0.02 | 0.03 |
| ABCA1 | ENSG00000165029 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.01 | 0.04 | 0.06 | 0.00 | 0.01 | 0.02 | 0.05 | 0.03 | 0.02 | 0.06 | 0.01 | 0.06 | 0.00 | 0.10 | 0.01 | 0.03 | 0.04 | 0.00 | 0.01 | 0.04 | 0.04 | 0.00 | 0.01 | 0.03 | 0.04 | 0.00 | 0.08 | 0.08 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.05 | 0.08 | 0.14 | 0.03 | 0.02 | 0.02 | 0.05 | 0.00 | 0.20 | 0.11 | 0.01 | 0.04 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.01 | 0.00 | 0.00 | 0.02 | 0.03 |
| CASP10 | ENSG00000003400 | 0.03 | 0.02 | 0.04 | 0.02 | 0.00 | 0.01 | 0.01 | 0.01 | 0.02 | 0.15 | 0.00 | 0.00 | 0.00 | 0.05 | 0.05 | 0.02 | 0.18 | 0.08 | 0.11 | 0.10 | 0.12 | 0.04 | 0.07 | 0.04 | 0.02 | 0.01 | 0.03 | 0.00 | 0.07 | 0.00 | 0.06 | 0.01 | 0.00 | 0.01 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.03 | 0.29 | 0.08 | 0.12 | 0.16 | 0.05 | 0.02 | 0.06 | 0.05 | 0.06 | 0.10 | 0.07 | 0.00 | 0.00 | 0.01 | 0.00 | 0.04 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.02 | 0.02 | 0.04 |
| TDRD5 | ENSG00000162782 | 0.02 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.02 | 0.02 | 0.22 | 0.02 | 0.02 | 0.00 | 0.07 | 0.03 | 0.11 | 0.00 | 0.19 | 0.01 | 0.03 | 0.00 | 0.16 | 0.03 | 0.10 | 0.01 | 0.03 | 0.00 | 0.13 | 0.01 | 0.04 | 0.00 | 0.16 | 0.01 | 0.20 | 0.01 | 0.00 | 0.04 | 0.02 | 0.00 | 0.00 | 0.00 | 0.17 | 0.01 | 0.36 | 0.03 | 0.08 | 0.01 | 0.08 | 0.00 | 0.25 | 0.00 | 0.21 | 0.03 | 0.07 | 0.00 | 0.00 | 0.00 | 0.32 | 0.00 | 0.01 | 0.00 | 0.01 | 0.01 | 0.02 | 0.00 | 0.10 | 0.03 |
| GGCX | ENSG00000115486 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.02 | 0.09 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.04 | 0.01 | 0.13 | 0.01 | 0.08 | 0.01 | 0.12 | 0.01 | 0.06 | 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 | 0.15 | 0.04 | 0.07 | 0.00 | 0.08 | 0.01 | 0.15 | 0.03 | 0.26 | 0.03 | 0.03 | 0.04 | 0.00 | 0.00 | 0.04 | 0.04 | 0.00 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 |
| FPR2 | ENSG00000171049 | 0.01 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.02 | 0.00 | 0.16 | 0.03 | 0.00 | 0.00 | 0.00 | 0.08 | 0.02 | 0.07 | 0.07 | 0.09 | 0.03 | 0.02 | 0.06 | 0.04 | 0.11 | 0.04 | 0.02 | 0.03 | 0.01 | 0.03 | 0.03 | 0.05 | 0.04 | 0.03 | 0.00 | 0.07 | 0.23 | 0.00 | 0.00 | 0.03 | 0.00 | 0.00 | 0.15 | 0.03 | 0.11 | 0.31 | 0.08 | 0.07 | 0.04 | 0.06 | 0.21 | 0.11 | 0.04 | 0.20 | 0.00 | 0.06 | 0.01 | 0.00 | 0.13 | 0.03 | 0.01 | 0.16 | 0.03 | 0.14 | 0.00 | 0.00 | 0.04 | 0.03 |
| PYGB | ENSG00000100994 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.01 | 0.02 | 0.04 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.08 | 0.02 | 0.07 | 0.02 | 0.06 | 0.02 | 0.10 | 0.03 | 0.06 | 0.02 | 0.07 | 0.00 | 0.06 | 0.02 | 0.02 | 0.01 | 0.02 | 0.00 | 0.06 | 0.01 | 0.03 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.05 | 0.04 | 0.10 | 0.03 | 0.06 | 0.02 | 0.03 | 0.01 | 0.20 | 0.01 | 0.06 | 0.03 | 0.02 | 0.00 | 0.01 | 0.00 | 0.04 | 0.02 | 0.01 | 0.01 | 0.02 | 0.01 | 0.02 | 0.00 | 0.02 | 0.02 |
| PREP | ENSG00000085377 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.30 | 0.09 | 0.11 | 0.00 | 0.01 | 0.00 | 0.15 | 0.01 | 0.05 | 0.05 | 0.04 | 0.04 | 0.03 | 0.06 | 0.08 | 0.08 | 0.06 | 0.01 | 0.03 | 0.03 | 0.02 | 0.00 | 0.04 | 0.01 | 0.08 | 0.00 | 0.15 | 0.07 | 0.04 | 0.00 | 0.01 | 0.00 | 0.00 | 0.21 | 0.08 | 0.16 | 0.19 | 0.03 | 0.01 | 0.05 | 0.02 | 0.29 | 0.03 | 0.11 | 0.09 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.30 | 0.02 | 0.01 | 0.00 | 0.04 | 0.06 | 0.03 | 0.00 | 0.11 |
| FGB | ENSG00000171564 | 0.01 | 0.02 | 0.00 | 0.01 | 0.06 | 0.00 | 0.01 | 0.02 | 0.05 | 0.11 | 0.00 | 0.02 | 0.00 | 0.01 | 0.05 | 0.06 | 0.01 | 0.11 | 0.01 | 0.09 | 0.05 | 0.06 | 0.05 | 0.07 | 0.01 | 0.06 | 0.02 | 0.04 | 0.01 | 0.04 | 0.09 | 0.06 | 0.00 | 0.12 | 0.10 | 0.05 | 0.00 | 0.03 | 0.00 | 0.00 | 0.06 | 0.07 | 0.07 | 0.26 | 0.03 | 0.08 | 0.04 | 0.05 | 0.06 | 0.05 | 0.11 | 0.10 | 0.01 | 0.01 | 0.00 | 0.00 | 0.03 | 0.03 | 0.00 | 0.09 | 0.00 | 0.03 | 0.00 | 0.00 | 0.04 | 0.05 |
| SLC26A11 | ENSG00000181045 | 0.02 | 0.00 | 0.05 | 0.00 | 0.02 | 0.00 | 0.03 | 0.03 | 0.20 | 0.00 | 0.00 | 0.00 | 0.09 | 0.02 | 0.18 | 0.01 | 0.22 | 0.04 | 0.07 | 0.05 | 0.17 | 0.08 | 0.09 | 0.04 | 0.05 | 0.01 | 0.04 | 0.03 | 0.02 | 0.09 | 0.29 | 0.01 | 0.10 | 0.01 | 0.23 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.35 | 0.03 | 0.42 | 0.03 | 0.11 | 0.09 | 0.16 | 0.02 | 0.54 | 0.08 | 0.19 | 0.05 | 0.06 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.07 | 0.01 | 0.04 | 0.01 | 0.17 | 0.00 | 0.24 | 0.02 |
| BMP3 | ENSG00000152785 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.03 | 0.02 | 0.08 | 0.04 | 0.00 | 0.00 | 0.02 | 0.08 | 0.04 | 0.03 | 0.09 | 0.04 | 0.04 | 0.03 | 0.03 | 0.07 | 0.03 | 0.05 | 0.01 | 0.01 | 0.03 | 0.01 | 0.01 | 0.00 | 0.01 | 0.10 | 0.05 | 0.03 | 0.06 | 0.02 | 0.02 | 0.02 | 0.00 | 0.00 | 0.05 | 0.03 | 0.08 | 0.20 | 0.03 | 0.03 | 0.02 | 0.02 | 0.02 | 0.09 | 0.05 | 0.05 | 0.00 | 0.02 | 0.00 | 0.01 | 0.00 | 0.05 | 0.00 | 0.02 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.02 |
| MTMR6 | ENSG00000139505 | 0.01 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.03 | 0.09 | 0.05 | 0.00 | 0.02 | 0.00 | 0.18 | 0.01 | 0.11 | 0.02 | 0.12 | 0.02 | 0.13 | 0.06 | 0.10 | 0.07 | 0.04 | 0.23 | 0.00 | 0.24 | 0.02 | 0.00 | 0.00 | 0.03 | 0.11 | 0.00 | 0.15 | 0.00 | 0.09 | 0.00 | 0.00 | 0.00 | 0.01 | 0.08 | 0.07 | 0.08 | 0.18 | 0.03 | 0.13 | 0.02 | 0.05 | 0.01 | 0.16 | 0.13 | 0.19 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.05 | 0.01 | 0.06 | 0.01 | 0.06 | 0.00 | 0.00 | 0.05 | 0.03 |
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