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 |
| HUNK | ENSG00000142149 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.07 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.03 | 0.03 | 0.03 | 0.03 | 0.00 | 0.02 | 0.04 | 0.05 | 0.03 | 0.02 | 0.01 | 0.01 | 0.00 | 0.08 | 0.01 | 0.01 | 0.01 | 0.02 | 0.00 | 0.03 | 0.10 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.03 | 0.10 | 0.08 | 0.01 | 0.05 | 0.03 | 0.01 | 0.06 | 0.05 | 0.11 | 0.04 | 0.02 | 0.00 | 0.04 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.02 | 0.03 | 0.00 | 0.02 | 0.01 |
| KCNC2 | ENSG00000166006 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.02 | 0.03 | 0.02 | 0.08 | 0.05 | 0.00 | 0.00 | 0.01 | 0.00 | 0.09 | 0.03 | 0.05 | 0.03 | 0.01 | 0.04 | 0.12 | 0.07 | 0.01 | 0.03 | 0.00 | 0.02 | 0.01 | 0.06 | 0.00 | 0.05 | 0.03 | 0.01 | 0.05 | 0.01 | 0.11 | 0.02 | 0.05 | 0.04 | 0.00 | 0.00 | 0.12 | 0.03 | 0.09 | 0.15 | 0.01 | 0.02 | 0.02 | 0.03 | 0.07 | 0.10 | 0.65 | 0.06 | 0.04 | 0.00 | 0.00 | 0.00 | 0.07 | 0.04 | 0.01 | 0.02 | 0.03 | 0.06 | 0.02 | 0.00 | 0.04 | 0.04 |
| MAPK6 | ENSG00000069956 | 0.00 | 0.00 | 0.00 | 0.01 | 0.14 | 0.01 | 0.00 | 0.04 | 0.05 | 0.03 | 0.00 | 0.00 | 0.08 | 0.12 | 0.01 | 0.04 | 0.03 | 0.05 | 0.04 | 0.03 | 0.03 | 0.02 | 0.02 | 0.06 | 0.01 | 0.03 | 0.00 | 0.05 | 0.00 | 0.02 | 0.04 | 0.03 | 0.00 | 0.01 | 0.02 | 0.03 | 0.00 | 0.01 | 0.00 | 0.00 | 0.07 | 0.08 | 0.10 | 0.19 | 0.01 | 0.10 | 0.01 | 0.07 | 0.09 | 0.28 | 0.07 | 0.04 | 0.02 | 0.02 | 0.00 | 0.00 | 0.06 | 0.05 | 0.00 | 0.02 | 0.01 | 0.07 | 0.00 | 0.00 | 0.03 | 0.09 |
| VARS2 | ENSG00000137411 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.17 | 0.02 | 0.00 | 0.00 | 0.02 | 0.02 | 0.09 | 0.01 | 0.07 | 0.05 | 0.04 | 0.04 | 0.20 | 0.05 | 0.12 | 0.04 | 0.04 | 0.01 | 0.07 | 0.01 | 0.03 | 0.01 | 0.12 | 0.01 | 0.08 | 0.03 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.09 | 0.03 | 0.31 | 0.06 | 0.17 | 0.01 | 0.05 | 0.01 | 0.16 | 0.03 | 0.08 | 0.05 | 0.01 | 0.01 | 0.01 | 0.00 | 0.05 | 0.14 | 0.01 | 0.00 | 0.00 | 0.01 | 0.13 | 0.00 | 0.13 | 0.01 |
| PHOSPHO1 | ENSG00000173868 | 0.00 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.11 | 0.02 | 0.00 | 0.00 | 0.09 | 0.01 | 0.08 | 0.01 | 0.09 | 0.01 | 0.02 | 0.01 | 0.12 | 0.03 | 0.08 | 0.01 | 0.03 | 0.01 | 0.06 | 0.04 | 0.03 | 0.02 | 0.05 | 0.01 | 0.02 | 0.01 | 0.01 | 0.04 | 0.01 | 0.05 | 0.00 | 0.00 | 0.50 | 0.03 | 0.16 | 0.05 | 0.06 | 0.00 | 0.06 | 0.04 | 0.27 | 0.04 | 0.09 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.01 | 0.01 | 0.03 | 0.03 | 0.13 | 0.01 |
| SLC28A3 | ENSG00000197506 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.03 | 0.03 | 0.00 | 0.02 | 0.01 | 0.06 | 0.00 | 0.03 | 0.03 | 0.03 | 0.01 | 0.01 | 0.06 | 0.01 | 0.03 | 0.03 | 0.01 | 0.01 | 0.02 | 0.01 | 0.00 | 0.00 | 0.01 | 0.02 | 0.00 | 0.15 | 0.02 | 0.00 | 0.02 | 0.02 | 0.00 | 0.00 | 0.03 | 0.03 | 0.05 | 0.12 | 0.00 | 0.03 | 0.03 | 0.03 | 0.04 | 0.15 | 0.14 | 0.00 | 0.03 | 0.02 | 0.00 | 0.03 | 0.05 | 0.02 | 0.00 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.02 | 0.02 |
| CLCN4 | ENSG00000073464 | 0.00 | 0.00 | 0.01 | 0.02 | 0.00 | 0.04 | 0.05 | 0.01 | 0.07 | 0.06 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.08 | 0.09 | 0.10 | 0.02 | 0.04 | 0.05 | 0.10 | 0.07 | 0.12 | 0.01 | 0.02 | 0.13 | 0.02 | 0.00 | 0.01 | 0.02 | 0.02 | 0.00 | 0.01 | 0.07 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.05 | 0.04 | 0.12 | 0.20 | 0.07 | 0.01 | 0.04 | 0.03 | 0.13 | 0.23 | 0.10 | 0.08 | 0.05 | 0.01 | 0.00 | 0.00 | 0.00 | 0.04 | 0.01 | 0.03 | 0.01 | 0.01 | 0.00 | 0.00 | 0.04 | 0.03 |
| PTPRK | ENSG00000152894 | 0.00 | 0.05 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.05 | 0.07 | 0.06 | 0.00 | 0.04 | 0.02 | 0.17 | 0.04 | 0.05 | 0.08 | 0.06 | 0.05 | 0.03 | 0.14 | 0.04 | 0.06 | 0.04 | 0.03 | 0.03 | 0.03 | 0.08 | 0.00 | 0.02 | 0.01 | 0.10 | 0.00 | 0.16 | 0.03 | 0.04 | 0.01 | 0.03 | 0.00 | 0.00 | 0.12 | 0.06 | 0.08 | 0.27 | 0.01 | 0.03 | 0.05 | 0.02 | 0.08 | 0.03 | 0.17 | 0.06 | 0.01 | 0.03 | 0.00 | 0.00 | 0.00 | 0.19 | 0.00 | 0.05 | 0.00 | 0.09 | 0.06 | 0.06 | 0.03 | 0.13 |
| SLC27A4 | ENSG00000167114 | 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 | 0.05 | 0.03 | 0.06 | 0.01 | 0.13 | 0.02 | 0.10 | 0.02 | 0.01 | 0.01 | 0.04 | 0.03 | 0.00 | 0.01 | 0.04 | 0.04 | 0.07 | 0.01 | 0.07 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.04 | 0.08 | 0.19 | 0.04 | 0.01 | 0.04 | 0.05 | 0.15 | 0.11 | 0.08 | 0.08 | 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 |
| GMPR | ENSG00000137198 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.01 | 0.41 | 0.04 | 0.00 | 0.01 | 0.01 | 0.02 | 0.07 | 0.01 | 0.08 | 0.07 | 0.04 | 0.05 | 0.10 | 0.16 | 0.05 | 0.08 | 0.02 | 0.04 | 0.02 | 0.03 | 0.02 | 0.06 | 0.15 | 0.02 | 0.06 | 0.03 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.16 | 0.04 | 0.51 | 0.04 | 0.10 | 0.06 | 0.07 | 0.02 | 0.23 | 0.03 | 0.04 | 0.13 | 0.03 | 0.01 | 0.00 | 0.00 | 0.05 | 0.01 | 0.02 | 0.01 | 0.01 | 0.01 | 0.28 | 0.00 | 0.20 | 0.00 |
| DNAJA1 | ENSG00000086061 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.02 | 0.07 | 0.04 | 0.00 | 0.00 | 0.01 | 0.11 | 0.06 | 0.02 | 0.33 | 0.04 | 0.13 | 0.04 | 0.21 | 0.03 | 0.12 | 0.03 | 0.01 | 0.00 | 0.01 | 0.00 | 0.04 | 0.01 | 0.01 | 0.01 | 0.19 | 0.01 | 0.14 | 0.07 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.03 | 0.09 | 0.09 | 0.01 | 0.01 | 0.04 | 0.02 | 0.04 | 0.05 | 0.07 | 0.05 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.04 | 0.08 | 0.00 | 0.00 | 0.05 | 0.05 |
| ICAM1 | ENSG00000090339 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.10 | 0.04 | 0.00 | 0.01 | 0.09 | 0.01 | 0.02 | 0.04 | 0.08 | 0.06 | 0.05 | 0.04 | 0.06 | 0.06 | 0.04 | 0.04 | 0.02 | 0.01 | 0.02 | 0.04 | 0.01 | 0.03 | 0.03 | 0.12 | 0.00 | 0.01 | 0.13 | 0.03 | 0.01 | 0.00 | 0.00 | 0.01 | 0.10 | 0.04 | 0.59 | 0.19 | 0.12 | 0.06 | 0.21 | 0.08 | 0.64 | 0.18 | 0.27 | 0.03 | 0.02 | 0.00 | 0.03 | 0.00 | 0.00 | 0.03 | 0.01 | 0.00 | 0.05 | 0.00 | 0.04 | 0.02 | 0.03 | 0.01 |
| SIDT2 | ENSG00000149577 | 0.00 | 0.01 | 0.00 | 0.06 | 0.02 | 0.02 | 0.01 | 0.09 | 0.03 | 0.11 | 0.00 | 0.00 | 0.02 | 0.05 | 0.05 | 0.08 | 0.04 | 0.09 | 0.03 | 0.16 | 0.04 | 0.12 | 0.06 | 0.08 | 0.01 | 0.01 | 0.00 | 0.03 | 0.01 | 0.01 | 0.01 | 0.09 | 0.00 | 0.17 | 0.00 | 0.05 | 0.00 | 0.06 | 0.00 | 0.00 | 0.02 | 0.24 | 0.15 | 0.16 | 0.04 | 0.29 | 0.04 | 0.05 | 0.12 | 0.18 | 0.03 | 0.23 | 0.00 | 0.15 | 0.02 | 0.00 | 0.11 | 0.01 | 0.04 | 0.01 | 0.01 | 0.01 | 0.00 | 0.07 | 0.00 | 0.27 |
| PRELP | ENSG00000188783 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.05 | 0.06 | 0.02 | 0.00 | 0.10 | 0.00 | 0.14 | 0.00 | 0.11 | 0.01 | 0.05 | 0.00 | 0.17 | 0.06 | 0.06 | 0.01 | 0.04 | 0.00 | 0.12 | 0.01 | 0.00 | 0.00 | 0.19 | 0.01 | 0.18 | 0.02 | 0.04 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.27 | 0.00 | 0.34 | 0.07 | 0.06 | 0.00 | 0.12 | 0.01 | 0.17 | 0.00 | 0.09 | 0.12 | 0.05 | 0.00 | 0.01 | 0.00 | 0.26 | 0.02 | 0.08 | 0.01 | 0.25 | 0.00 | 0.09 | 0.00 | 0.18 | 0.01 |
| FGF10 | ENSG00000070193 | 0.01 | 0.00 | 0.01 | 0.01 | 0.03 | 0.00 | 0.01 | 0.02 | 0.14 | 0.01 | 0.00 | 0.00 | 0.01 | 0.01 | 0.18 | 0.01 | 0.22 | 0.01 | 0.10 | 0.01 | 0.23 | 0.02 | 0.17 | 0.02 | 0.05 | 0.01 | 0.03 | 0.01 | 0.04 | 0.00 | 0.03 | 0.00 | 0.00 | 0.01 | 0.21 | 0.01 | 0.01 | 0.03 | 0.00 | 0.00 | 0.10 | 0.02 | 0.19 | 0.02 | 0.08 | 0.00 | 0.06 | 0.01 | 0.16 | 0.03 | 0.20 | 0.02 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.00 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.09 | 0.03 |
| ADGRL1 | ENSG00000072071 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.02 | 0.05 | 0.00 | 0.00 | 0.06 | 0.02 | 0.01 | 0.05 | 0.12 | 0.04 | 0.07 | 0.02 | 0.14 | 0.04 | 0.05 | 0.02 | 0.01 | 0.00 | 0.01 | 0.03 | 0.01 | 0.01 | 0.06 | 0.06 | 0.00 | 0.03 | 0.21 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.10 | 0.03 | 0.86 | 0.06 | 0.09 | 0.01 | 0.21 | 0.02 | 0.27 | 0.11 | 0.26 | 0.02 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 | 0.00 | 0.02 | 0.00 | 0.02 | 0.00 | 0.02 | 0.02 |
| PRIMPOL | ENSG00000164306 | 0.00 | 0.03 | 0.00 | 0.01 | 0.10 | 0.04 | 0.03 | 0.03 | 0.04 | 0.17 | 0.00 | 0.02 | 0.00 | 0.07 | 0.02 | 0.13 | 0.03 | 0.19 | 0.03 | 0.13 | 0.07 | 0.11 | 0.02 | 0.24 | 0.01 | 0.14 | 0.02 | 0.13 | 0.00 | 0.06 | 0.07 | 0.23 | 0.00 | 0.35 | 0.20 | 0.18 | 0.00 | 0.05 | 0.00 | 0.00 | 0.05 | 0.12 | 0.07 | 0.38 | 0.04 | 0.12 | 0.03 | 0.09 | 0.09 | 0.16 | 0.04 | 0.32 | 0.02 | 0.00 | 0.00 | 0.00 | 0.03 | 0.16 | 0.00 | 0.10 | 0.00 | 0.09 | 0.00 | 0.00 | 0.05 | 0.10 |
| SLCO3A1 | ENSG00000176463 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.02 | 0.01 | 0.04 | 0.03 | 0.03 | 0.00 | 0.06 | 0.00 | 0.07 | 0.02 | 0.21 | 0.02 | 0.07 | 0.03 | 0.25 | 0.03 | 0.26 | 0.02 | 0.05 | 0.01 | 0.07 | 0.04 | 0.06 | 0.00 | 0.07 | 0.06 | 0.05 | 0.01 | 0.07 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.18 | 0.02 | 0.35 | 0.09 | 0.18 | 0.01 | 0.05 | 0.02 | 0.22 | 0.05 | 0.17 | 0.04 | 0.00 | 0.01 | 0.00 | 0.01 | 0.06 | 0.00 | 0.02 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.20 | 0.01 |
| MBD5 | ENSG00000204406 | 0.01 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.17 | 0.03 | 0.06 | 0.00 | 0.01 | 0.00 | 0.01 | 0.03 | 0.03 | 0.06 | 0.05 | 0.03 | 0.02 | 0.07 | 0.04 | 0.02 | 0.07 | 0.00 | 0.04 | 0.00 | 0.02 | 0.02 | 0.05 | 0.01 | 0.13 | 0.05 | 0.05 | 0.02 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.07 | 0.19 | 0.10 | 0.05 | 0.02 | 0.05 | 0.01 | 0.07 | 0.09 | 0.08 | 0.06 | 0.01 | 0.02 | 0.00 | 0.00 | 0.00 | 0.21 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.03 | 0.01 |
| PTPDC1 | ENSG00000158079 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 | 0.06 | 0.04 | 0.00 | 0.01 | 0.01 | 0.04 | 0.01 | 0.04 | 0.03 | 0.02 | 0.04 | 0.00 | 0.09 | 0.01 | 0.02 | 0.05 | 0.01 | 0.01 | 0.04 | 0.02 | 0.00 | 0.01 | 0.01 | 0.04 | 0.00 | 0.08 | 0.04 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.03 | 0.03 | 0.07 | 0.14 | 0.02 | 0.02 | 0.03 | 0.04 | 0.01 | 0.11 | 0.10 | 0.01 | 0.05 | 0.02 | 0.00 | 0.02 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.03 |
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