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 |
| PRKCSH | ENSG00000130175 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.06 | 0.04 | 0.00 | 0.01 | 0.09 | 0.01 | 0.01 | 0.05 | 0.05 | 0.06 | 0.05 | 0.04 | 0.06 | 0.06 | 0.06 | 0.02 | 0.02 | 0.01 | 0.02 | 0.02 | 0.01 | 0.03 | 0.03 | 0.09 | 0.00 | 0.01 | 0.12 | 0.03 | 0.00 | 0.00 | 0.00 | 0.01 | 0.07 | 0.04 | 0.59 | 0.19 | 0.10 | 0.04 | 0.22 | 0.03 | 0.27 | 0.15 | 0.22 | 0.01 | 0.02 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.04 | 0.00 | 0.02 | 0.02 | 0.02 | 0.02 |
| PDGFB | ENSG00000100311 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.01 | 0.07 | 0.06 | 0.00 | 0.05 | 0.00 | 0.02 | 0.06 | 0.03 | 0.08 | 0.02 | 0.03 | 0.01 | 0.03 | 0.01 | 0.02 | 0.02 | 0.01 | 0.02 | 0.01 | 0.02 | 0.01 | 0.02 | 0.04 | 0.02 | 0.00 | 0.01 | 0.02 | 0.01 | 0.00 | 0.05 | 0.00 | 0.00 | 0.03 | 0.02 | 0.11 | 0.13 | 0.04 | 0.02 | 0.09 | 0.02 | 0.16 | 0.10 | 0.08 | 0.03 | 0.01 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.02 | 0.01 | 0.04 | 0.02 | 0.00 | 0.21 | 0.01 |
| PHF10 | ENSG00000130024 | 0.00 | 0.06 | 0.00 | 0.02 | 0.00 | 0.05 | 0.00 | 0.05 | 0.04 | 0.09 | 0.00 | 0.01 | 0.04 | 0.09 | 0.02 | 0.07 | 0.10 | 0.07 | 0.05 | 0.04 | 0.14 | 0.04 | 0.09 | 0.09 | 0.02 | 0.02 | 0.03 | 0.02 | 0.00 | 0.03 | 0.02 | 0.19 | 0.06 | 0.24 | 0.10 | 0.05 | 0.00 | 0.04 | 0.01 | 0.00 | 0.06 | 0.13 | 0.08 | 0.46 | 0.02 | 0.10 | 0.03 | 0.05 | 0.24 | 0.10 | 0.17 | 0.10 | 0.01 | 0.05 | 0.00 | 0.00 | 0.03 | 0.02 | 0.00 | 0.05 | 0.02 | 0.12 | 0.05 | 0.06 | 0.02 | 0.17 |
| USP21 | ENSG00000143258 | 0.03 | 0.00 | 0.01 | 0.01 | 0.00 | 0.03 | 0.02 | 0.04 | 0.96 | 0.00 | 0.02 | 0.00 | 0.10 | 0.01 | 0.27 | 0.00 | 0.28 | 0.00 | 0.06 | 0.00 | 0.33 | 0.00 | 0.14 | 0.00 | 0.03 | 0.00 | 0.14 | 0.00 | 0.06 | 0.00 | 0.31 | 0.00 | 0.30 | 0.01 | 0.16 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.33 | 0.00 | 0.37 | 0.02 | 0.18 | 0.00 | 0.16 | 0.00 | 0.41 | 0.00 | 0.43 | 0.02 | 0.10 | 0.00 | 0.00 | 0.00 | 0.25 | 0.00 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.17 | 0.01 |
| PDK2 | ENSG00000005882 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.13 | 0.01 | 0.00 | 0.00 | 0.09 | 0.00 | 0.09 | 0.01 | 0.12 | 0.01 | 0.02 | 0.01 | 0.17 | 0.01 | 0.10 | 0.01 | 0.03 | 0.01 | 0.06 | 0.04 | 0.06 | 0.02 | 0.05 | 0.01 | 0.02 | 0.01 | 0.08 | 0.04 | 0.01 | 0.03 | 0.00 | 0.00 | 0.51 | 0.03 | 0.19 | 0.04 | 0.09 | 0.00 | 0.08 | 0.03 | 0.23 | 0.02 | 0.12 | 0.03 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.02 | 0.01 | 0.03 | 0.03 | 0.12 | 0.01 |
| DNAJC16 | ENSG00000116138 | 0.00 | 0.06 | 0.01 | 0.08 | 0.00 | 0.00 | 0.01 | 0.04 | 0.10 | 0.08 | 0.00 | 0.03 | 0.04 | 0.26 | 0.06 | 0.06 | 0.06 | 0.11 | 0.04 | 0.10 | 0.10 | 0.09 | 0.09 | 0.08 | 0.01 | 0.15 | 0.00 | 0.21 | 0.02 | 0.06 | 0.03 | 0.21 | 0.00 | 1.11 | 0.01 | 0.11 | 0.01 | 0.09 | 0.00 | 0.00 | 0.02 | 0.21 | 0.18 | 0.39 | 0.06 | 0.08 | 0.10 | 0.12 | 0.08 | 0.28 | 0.19 | 0.17 | 0.05 | 0.09 | 0.02 | 0.00 | 0.00 | 0.07 | 0.00 | 0.02 | 0.05 | 0.09 | 0.00 | 0.07 | 0.07 | 0.09 |
| ENG | ENSG00000106991 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.05 | 0.00 | 0.03 | 0.02 | 0.00 | 0.01 | 0.00 | 0.02 | 0.04 | 0.02 | 0.06 | 0.02 | 0.06 | 0.01 | 0.12 | 0.02 | 0.10 | 0.01 | 0.01 | 0.01 | 0.04 | 0.03 | 0.00 | 0.01 | 0.05 | 0.03 | 0.07 | 0.04 | 0.14 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.09 | 0.03 | 0.10 | 0.17 | 0.05 | 0.01 | 0.08 | 0.04 | 0.17 | 0.11 | 0.04 | 0.07 | 0.02 | 0.04 | 0.01 | 0.00 | 0.05 | 0.00 | 0.02 | 0.00 | 0.03 | 0.02 | 0.00 | 0.00 | 0.04 | 0.02 |
| PRCP | ENSG00000137509 | 0.00 | 0.01 | 0.00 | 0.01 | 0.04 | 0.03 | 0.04 | 0.01 | 0.14 | 0.02 | 0.00 | 0.00 | 0.08 | 0.02 | 0.12 | 0.01 | 0.10 | 0.02 | 0.17 | 0.04 | 0.22 | 0.02 | 0.09 | 0.02 | 0.02 | 0.00 | 0.02 | 0.01 | 0.00 | 0.01 | 0.03 | 0.03 | 0.00 | 0.02 | 0.01 | 0.00 | 0.02 | 0.02 | 0.00 | 0.00 | 0.17 | 0.06 | 0.53 | 0.05 | 0.19 | 0.02 | 0.10 | 0.03 | 0.07 | 0.14 | 0.13 | 0.06 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.02 | 0.03 | 0.01 | 0.00 | 0.00 | 0.10 | 0.06 |
| RRM2B | ENSG00000048392 | 0.01 | 0.00 | 0.01 | 0.00 | 0.21 | 0.00 | 0.08 | 0.01 | 0.70 | 0.00 | 0.02 | 0.00 | 0.02 | 0.01 | 0.22 | 0.01 | 0.23 | 0.01 | 0.17 | 0.00 | 0.37 | 0.00 | 0.23 | 0.00 | 0.13 | 0.00 | 0.21 | 0.00 | 0.04 | 0.01 | 0.31 | 0.00 | 0.25 | 0.01 | 0.04 | 0.00 | 0.00 | 0.03 | 0.00 | 0.00 | 0.48 | 0.01 | 0.70 | 0.07 | 0.14 | 0.00 | 0.12 | 0.01 | 0.48 | 0.00 | 0.17 | 0.04 | 0.09 | 0.00 | 0.00 | 0.00 | 0.04 | 0.04 | 0.14 | 0.00 | 0.01 | 0.01 | 0.42 | 0.00 | 0.13 | 0.01 |
| CHST10 | ENSG00000115526 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.01 | 0.11 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.05 | 0.01 | 0.11 | 0.01 | 0.07 | 0.01 | 0.12 | 0.02 | 0.06 | 0.02 | 0.00 | 0.01 | 0.05 | 0.00 | 0.00 | 0.01 | 0.01 | 0.01 | 0.00 | 0.01 | 0.08 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.02 | 0.16 | 0.06 | 0.03 | 0.01 | 0.05 | 0.02 | 0.17 | 0.00 | 0.13 | 0.03 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.06 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 |
| KLHL12 | ENSG00000117153 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.05 | 0.06 | 0.02 | 0.00 | 0.10 | 0.00 | 0.13 | 0.00 | 0.09 | 0.01 | 0.06 | 0.01 | 0.15 | 0.06 | 0.05 | 0.02 | 0.04 | 0.00 | 0.11 | 0.02 | 0.00 | 0.00 | 0.20 | 0.01 | 0.18 | 0.02 | 0.04 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.27 | 0.00 | 0.30 | 0.07 | 0.06 | 0.00 | 0.10 | 0.01 | 0.17 | 0.00 | 0.11 | 0.12 | 0.05 | 0.00 | 0.01 | 0.00 | 0.26 | 0.02 | 0.02 | 0.01 | 0.11 | 0.00 | 0.09 | 0.00 | 0.18 | 0.01 |
| ATP6V0A1 | ENSG00000033627 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.09 | 0.04 | 0.02 | 0.01 | 0.00 | 0.01 | 0.02 | 0.07 | 0.01 | 0.04 | 0.05 | 0.03 | 0.01 | 0.14 | 0.02 | 0.12 | 0.03 | 0.05 | 0.01 | 0.03 | 0.02 | 0.03 | 0.03 | 0.05 | 0.03 | 0.02 | 0.01 | 0.01 | 0.14 | 0.00 | 0.12 | 0.00 | 0.00 | 0.06 | 0.10 | 0.02 | 0.15 | 0.02 | 0.03 | 0.03 | 0.08 | 0.01 | 0.20 | 0.06 | 0.10 | 0.01 | 0.01 | 0.00 | 0.02 | 0.02 | 0.00 | 0.00 | 0.01 | 0.01 | 0.02 | 0.00 | 0.05 | 0.01 | 0.03 |
| MATN2 | ENSG00000132561 | 0.00 | 0.00 | 0.01 | 0.00 | 0.14 | 0.00 | 0.10 | 0.01 | 0.43 | 0.00 | 0.02 | 0.00 | 0.02 | 0.01 | 0.21 | 0.02 | 0.20 | 0.02 | 0.12 | 0.00 | 0.27 | 0.01 | 0.19 | 0.00 | 0.09 | 0.00 | 0.19 | 0.00 | 0.04 | 0.01 | 0.28 | 0.00 | 0.25 | 0.01 | 0.04 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.41 | 0.00 | 0.61 | 0.06 | 0.11 | 0.00 | 0.10 | 0.01 | 0.60 | 0.02 | 0.15 | 0.05 | 0.11 | 0.00 | 0.00 | 0.00 | 0.08 | 0.02 | 0.13 | 0.00 | 0.02 | 0.00 | 0.42 | 0.00 | 0.13 | 0.01 |
| AKAP1 | ENSG00000121057 | 0.01 | 0.00 | 0.05 | 0.00 | 0.00 | 0.00 | 0.03 | 0.03 | 0.17 | 0.02 | 0.02 | 0.00 | 0.12 | 0.00 | 0.09 | 0.01 | 0.15 | 0.02 | 0.04 | 0.02 | 0.16 | 0.03 | 0.05 | 0.02 | 0.02 | 0.02 | 0.06 | 0.05 | 0.01 | 0.12 | 0.11 | 0.01 | 0.12 | 0.01 | 0.10 | 0.03 | 0.02 | 0.00 | 0.00 | 0.00 | 0.45 | 0.01 | 0.17 | 0.03 | 0.08 | 0.03 | 0.08 | 0.04 | 0.23 | 0.02 | 0.13 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.06 | 0.01 | 0.03 | 0.00 | 0.14 | 0.00 | 0.20 | 0.02 |
| FCGRT | ENSG00000104870 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.01 | 0.11 | 0.04 | 0.00 | 0.02 | 0.00 | 0.06 | 0.02 | 0.07 | 0.05 | 0.10 | 0.04 | 0.02 | 0.07 | 0.05 | 0.07 | 0.03 | 0.01 | 0.02 | 0.02 | 0.03 | 0.03 | 0.05 | 0.05 | 0.03 | 0.00 | 0.07 | 0.26 | 0.02 | 0.00 | 0.03 | 0.00 | 0.00 | 0.12 | 0.04 | 0.04 | 0.32 | 0.05 | 0.06 | 0.06 | 0.05 | 0.15 | 0.18 | 0.04 | 0.18 | 0.00 | 0.04 | 0.01 | 0.00 | 0.07 | 0.03 | 0.01 | 0.13 | 0.04 | 0.12 | 0.00 | 0.00 | 0.02 | 0.02 |
| HAGH | ENSG00000063854 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.02 | 0.15 | 0.00 | 0.00 | 0.04 | 0.02 | 0.05 | 0.05 | 0.03 | 0.07 | 0.03 | 0.03 | 0.04 | 0.10 | 0.03 | 0.07 | 0.03 | 0.03 | 0.05 | 0.03 | 0.02 | 0.02 | 0.04 | 0.03 | 0.00 | 0.05 | 0.20 | 0.02 | 0.00 | 0.02 | 0.00 | 0.00 | 0.09 | 0.02 | 0.11 | 0.19 | 0.10 | 0.04 | 0.05 | 0.03 | 0.27 | 0.08 | 0.08 | 0.04 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.04 | 0.01 | 0.00 | 0.02 | 0.02 | 0.00 | 0.00 | 0.04 | 0.02 |
| PWWP2B | ENSG00000171813 | 0.01 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.07 | 0.06 | 0.08 | 0.00 | 0.03 | 0.02 | 0.11 | 0.03 | 0.05 | 0.05 | 0.07 | 0.03 | 0.04 | 0.05 | 0.09 | 0.08 | 0.07 | 0.01 | 0.06 | 0.02 | 0.04 | 0.01 | 0.01 | 0.03 | 0.10 | 0.14 | 0.17 | 0.11 | 0.06 | 0.01 | 0.02 | 0.00 | 0.00 | 0.09 | 0.12 | 0.26 | 0.22 | 0.03 | 0.05 | 0.06 | 0.06 | 0.20 | 0.04 | 0.05 | 0.14 | 0.05 | 0.09 | 0.00 | 0.00 | 0.03 | 0.03 | 0.00 | 0.14 | 0.00 | 0.08 | 0.00 | 0.00 | 0.01 | 0.07 |
| PTGR1 | ENSG00000106853 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.04 | 0.05 | 0.00 | 0.01 | 0.02 | 0.02 | 0.05 | 0.02 | 0.04 | 0.01 | 0.05 | 0.00 | 0.12 | 0.01 | 0.05 | 0.02 | 0.00 | 0.01 | 0.04 | 0.02 | 0.00 | 0.01 | 0.04 | 0.04 | 0.06 | 0.04 | 0.14 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.05 | 0.09 | 0.12 | 0.02 | 0.01 | 0.03 | 0.03 | 0.00 | 0.15 | 0.07 | 0.01 | 0.03 | 0.02 | 0.01 | 0.00 | 0.05 | 0.00 | 0.00 | 0.01 | 0.02 | 0.01 | 0.00 | 0.00 | 0.04 | 0.01 |
| KBTBD2 | ENSG00000170852 | 0.00 | 0.00 | 0.03 | 0.01 | 0.00 | 0.00 | 0.05 | 0.00 | 0.10 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.06 | 0.00 | 0.09 | 0.02 | 0.04 | 0.01 | 0.13 | 0.02 | 0.03 | 0.00 | 0.04 | 0.00 | 0.03 | 0.00 | 0.01 | 0.00 | 0.04 | 0.00 | 0.00 | 0.02 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.11 | 0.02 | 0.14 | 0.11 | 0.01 | 0.00 | 0.05 | 0.01 | 0.07 | 0.00 | 0.14 | 0.03 | 0.05 | 0.00 | 0.00 | 0.01 | 0.00 | 0.02 | 0.03 | 0.00 | 0.07 | 0.00 | 0.00 | 0.00 | 0.06 | 0.02 |
| CLOCK | ENSG00000134852 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.01 | 0.02 | 0.10 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.10 | 0.02 | 0.51 | 0.01 | 0.09 | 0.01 | 0.14 | 0.05 | 0.04 | 0.04 | 0.03 | 0.01 | 0.04 | 0.03 | 0.03 | 0.02 | 0.03 | 0.05 | 0.00 | 0.08 | 0.03 | 0.00 | 0.02 | 0.02 | 0.00 | 0.00 | 0.09 | 0.01 | 0.21 | 0.05 | 0.13 | 0.01 | 0.04 | 0.00 | 0.15 | 0.05 | 0.22 | 0.03 | 0.33 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.13 | 0.01 | 0.32 | 0.02 | 0.00 | 0.00 | 0.09 | 0.01 |
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