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 |
| ULK1 | ENSG00000177169 | 0.01 | 0.01 | 0.03 | 0.01 | 0.07 | 0.02 | 0.02 | 0.08 | 0.09 | 0.07 | 0.00 | 0.00 | 0.05 | 0.03 | 0.06 | 0.07 | 0.05 | 0.07 | 0.02 | 0.05 | 0.10 | 0.07 | 0.06 | 0.05 | 0.02 | 0.01 | 0.05 | 0.02 | 0.00 | 0.06 | 0.05 | 0.11 | 0.00 | 0.17 | 0.11 | 0.02 | 0.03 | 0.04 | 0.00 | 0.00 | 0.04 | 0.09 | 0.13 | 0.30 | 0.03 | 0.02 | 0.04 | 0.07 | 0.04 | 0.16 | 0.23 | 0.09 | 0.01 | 0.01 | 0.00 | 0.00 | 0.09 | 0.00 | 0.03 | 0.02 | 0.02 | 0.02 | 0.00 | 0.00 | 0.03 | 0.08 |
| H6PD | ENSG00000049239 | 0.00 | 0.06 | 0.01 | 0.08 | 0.00 | 0.00 | 0.01 | 0.06 | 0.10 | 0.08 | 0.00 | 0.02 | 0.04 | 0.27 | 0.06 | 0.06 | 0.07 | 0.11 | 0.04 | 0.08 | 0.09 | 0.09 | 0.10 | 0.08 | 0.01 | 0.14 | 0.00 | 0.21 | 0.04 | 0.07 | 0.03 | 0.29 | 0.00 | 1.10 | 0.06 | 0.23 | 0.01 | 0.11 | 0.00 | 0.00 | 0.03 | 0.19 | 0.24 | 0.35 | 0.04 | 0.10 | 0.06 | 0.11 | 0.04 | 0.29 | 0.18 | 0.22 | 0.08 | 0.11 | 0.02 | 0.01 | 0.00 | 0.07 | 0.00 | 0.06 | 0.01 | 0.27 | 0.00 | 0.10 | 0.06 | 0.12 |
| CHRM3 | ENSG00000133019 | 0.01 | 0.02 | 0.01 | 0.02 | 0.00 | 0.00 | 0.01 | 0.07 | 0.11 | 0.04 | 0.02 | 0.02 | 0.05 | 0.03 | 0.11 | 0.01 | 0.14 | 0.02 | 0.08 | 0.01 | 0.20 | 0.05 | 0.11 | 0.03 | 0.03 | 0.02 | 0.07 | 0.02 | 0.01 | 0.01 | 0.18 | 0.02 | 0.23 | 0.02 | 0.06 | 0.03 | 0.00 | 0.05 | 0.00 | 0.00 | 0.26 | 0.02 | 0.50 | 0.09 | 0.10 | 0.02 | 0.11 | 0.01 | 0.40 | 0.00 | 0.06 | 0.25 | 0.04 | 0.02 | 0.02 | 0.00 | 0.06 | 0.12 | 0.01 | 0.04 | 0.02 | 0.06 | 0.08 | 0.03 | 0.18 | 0.03 |
| GALNS | ENSG00000141012 | 0.00 | 0.00 | 0.00 | 0.04 | 0.00 | 0.06 | 0.01 | 0.25 | 0.08 | 0.05 | 0.00 | 0.00 | 0.00 | 0.19 | 0.02 | 0.12 | 0.03 | 0.06 | 0.04 | 0.04 | 0.09 | 0.05 | 0.05 | 0.05 | 0.02 | 0.03 | 0.02 | 0.03 | 0.02 | 0.01 | 0.02 | 0.08 | 0.05 | 0.05 | 0.07 | 0.06 | 0.00 | 0.02 | 0.00 | 0.01 | 0.05 | 0.09 | 0.05 | 0.34 | 0.05 | 0.08 | 0.02 | 0.08 | 0.03 | 0.29 | 0.06 | 0.10 | 0.00 | 0.12 | 0.00 | 0.04 | 0.03 | 0.00 | 0.00 | 0.02 | 0.01 | 0.05 | 0.00 | 0.02 | 0.02 | 0.10 |
| CYP4F2 | ENSG00000186115 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.02 | 0.05 | 0.00 | 0.00 | 0.06 | 0.00 | 0.01 | 0.02 | 0.09 | 0.02 | 0.05 | 0.01 | 0.21 | 0.01 | 0.06 | 0.00 | 0.01 | 0.00 | 0.01 | 0.03 | 0.01 | 0.00 | 0.09 | 0.03 | 0.00 | 0.03 | 0.32 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.10 | 0.02 | 0.77 | 0.03 | 0.01 | 0.01 | 0.26 | 0.01 | 0.26 | 0.05 | 0.14 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.02 | 0.00 | 0.02 | 0.00 | 0.02 | 0.00 | 0.02 | 0.01 |
| USP30 | ENSG00000135093 | 0.01 | 0.01 | 0.02 | 0.00 | 0.06 | 0.02 | 0.04 | 0.04 | 0.09 | 0.03 | 0.00 | 0.00 | 0.02 | 0.00 | 0.02 | 0.05 | 0.02 | 0.04 | 0.02 | 0.03 | 0.08 | 0.05 | 0.05 | 0.02 | 0.00 | 0.01 | 0.01 | 0.01 | 0.00 | 0.06 | 0.05 | 0.04 | 0.00 | 0.22 | 0.11 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.03 | 0.07 | 0.09 | 0.20 | 0.01 | 0.02 | 0.01 | 0.05 | 0.08 | 0.07 | 0.14 | 0.05 | 0.00 | 0.01 | 0.00 | 0.00 | 0.10 | 0.00 | 0.00 | 0.04 | 0.01 | 0.02 | 0.00 | 0.00 | 0.02 | 0.07 |
| JAG1 | ENSG00000101384 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.00 | 0.02 | 0.03 | 0.02 | 0.00 | 0.00 | 0.00 | 0.05 | 0.04 | 0.04 | 0.16 | 0.01 | 0.11 | 0.03 | 0.06 | 0.02 | 0.04 | 0.03 | 0.04 | 0.04 | 0.06 | 0.08 | 0.00 | 0.01 | 0.02 | 0.01 | 0.00 | 0.03 | 0.03 | 0.05 | 0.00 | 0.01 | 0.00 | 0.00 | 0.05 | 0.05 | 0.20 | 0.07 | 0.03 | 0.02 | 0.04 | 0.01 | 0.07 | 0.09 | 0.09 | 0.04 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.02 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.02 | 0.02 |
| AMD1 | ENSG00000123505 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.30 | 0.02 | 0.12 | 0.00 | 0.01 | 0.00 | 0.14 | 0.01 | 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 | 0.07 | 0.26 | 0.02 | 0.02 | 0.08 | 0.02 | 0.13 | 0.04 | 0.22 | 0.08 | 0.00 | 0.04 | 0.00 | 0.00 | 0.01 | 0.21 | 0.00 | 0.02 | 0.02 | 0.06 | 0.00 | 0.03 | 0.00 | 0.13 |
| COQ6 | ENSG00000119723 | 0.00 | 0.03 | 0.00 | 0.01 | 0.00 | 0.01 | 0.01 | 0.05 | 0.04 | 0.05 | 0.00 | 0.01 | 0.00 | 0.08 | 0.03 | 0.05 | 0.05 | 0.03 | 0.04 | 0.01 | 0.05 | 0.02 | 0.02 | 0.04 | 0.00 | 0.03 | 0.01 | 0.03 | 0.01 | 0.01 | 0.01 | 0.10 | 0.00 | 0.33 | 0.01 | 0.05 | 0.01 | 0.04 | 0.00 | 0.00 | 0.01 | 0.10 | 0.08 | 0.20 | 0.05 | 0.02 | 0.03 | 0.02 | 0.17 | 0.06 | 0.06 | 0.14 | 0.03 | 0.01 | 0.00 | 0.00 | 0.04 | 0.00 | 0.00 | 0.12 | 0.03 | 0.08 | 0.03 | 0.00 | 0.00 | 0.05 |
| SLC38A4 | ENSG00000139209 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.05 | 0.04 | 0.00 | 0.00 | 0.00 | 0.05 | 0.05 | 0.03 | 0.11 | 0.02 | 0.03 | 0.03 | 0.06 | 0.05 | 0.08 | 0.04 | 0.02 | 0.00 | 0.06 | 0.05 | 0.01 | 0.03 | 0.03 | 0.01 | 0.00 | 0.01 | 0.23 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.05 | 0.05 | 0.24 | 0.06 | 0.04 | 0.01 | 0.11 | 0.01 | 0.13 | 0.10 | 0.20 | 0.10 | 0.02 | 0.02 | 0.00 | 0.02 | 0.13 | 0.00 | 0.01 | 0.05 | 0.03 | 0.06 | 0.00 | 0.00 | 0.10 | 0.05 |
| IL1RL2 | ENSG00000115598 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.10 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.02 | 0.10 | 0.01 | 0.07 | 0.01 | 0.15 | 0.02 | 0.07 | 0.02 | 0.00 | 0.01 | 0.02 | 0.00 | 0.01 | 0.01 | 0.01 | 0.01 | 0.00 | 0.01 | 0.03 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.03 | 0.19 | 0.07 | 0.04 | 0.01 | 0.05 | 0.01 | 0.09 | 0.00 | 0.12 | 0.04 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.05 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 |
| TRPV6 | ENSG00000165125 | 0.02 | 0.01 | 0.05 | 0.00 | 0.05 | 0.02 | 0.02 | 0.03 | 0.05 | 0.03 | 0.00 | 0.01 | 0.04 | 0.03 | 0.07 | 0.02 | 0.08 | 0.06 | 0.02 | 0.15 | 0.04 | 0.20 | 0.03 | 0.09 | 0.02 | 0.01 | 0.03 | 0.02 | 0.03 | 0.04 | 0.04 | 0.05 | 0.00 | 0.11 | 0.06 | 0.06 | 0.00 | 0.02 | 0.00 | 0.00 | 0.09 | 0.04 | 0.55 | 0.04 | 0.03 | 0.09 | 0.04 | 0.05 | 0.05 | 0.14 | 0.12 | 0.11 | 0.02 | 0.04 | 0.00 | 0.05 | 0.02 | 0.09 | 0.10 | 0.01 | 0.04 | 0.02 | 0.00 | 0.03 | 0.21 | 0.02 |
| MARCO | ENSG00000019169 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.12 | 0.04 | 0.02 | 0.00 | 0.00 | 0.02 | 0.00 | 0.05 | 0.01 | 0.11 | 0.01 | 0.12 | 0.01 | 0.30 | 0.02 | 0.07 | 0.03 | 0.00 | 0.01 | 0.00 | 0.01 | 0.01 | 0.01 | 0.02 | 0.04 | 0.00 | 0.01 | 0.05 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.04 | 0.11 | 0.12 | 0.03 | 0.00 | 0.04 | 0.02 | 0.09 | 0.00 | 0.15 | 0.02 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.08 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.00 |
| KCNJ4 | ENSG00000168135 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.10 | 0.05 | 0.00 | 0.05 | 0.00 | 0.03 | 0.07 | 0.03 | 0.10 | 0.02 | 0.03 | 0.01 | 0.03 | 0.02 | 0.02 | 0.02 | 0.01 | 0.02 | 0.01 | 0.02 | 0.02 | 0.02 | 0.07 | 0.00 | 0.00 | 0.01 | 0.02 | 0.01 | 0.00 | 0.04 | 0.00 | 0.00 | 0.04 | 0.03 | 0.12 | 0.11 | 0.03 | 0.01 | 0.09 | 0.02 | 0.23 | 0.10 | 0.06 | 0.03 | 0.01 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.02 | 0.03 | 0.02 | 0.00 | 0.20 | 0.01 |
| SIGLEC12 | ENSG00000254521 | 0.01 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.02 | 0.00 | 0.14 | 0.03 | 0.00 | 0.00 | 0.00 | 0.06 | 0.02 | 0.08 | 0.07 | 0.09 | 0.03 | 0.02 | 0.06 | 0.03 | 0.08 | 0.03 | 0.02 | 0.02 | 0.01 | 0.03 | 0.04 | 0.04 | 0.04 | 0.03 | 0.00 | 0.07 | 0.23 | 0.02 | 0.00 | 0.03 | 0.00 | 0.00 | 0.14 | 0.03 | 0.10 | 0.30 | 0.07 | 0.07 | 0.04 | 0.05 | 0.16 | 0.14 | 0.04 | 0.19 | 0.00 | 0.06 | 0.01 | 0.00 | 0.13 | 0.03 | 0.01 | 0.16 | 0.03 | 0.13 | 0.00 | 0.00 | 0.03 | 0.03 |
| CHST7 | ENSG00000147119 | 0.01 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.03 | 0.00 | 0.06 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.10 | 0.02 | 0.08 | 0.03 | 0.04 | 0.02 | 0.04 | 0.04 | 0.05 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.01 | 0.01 | 0.00 | 0.01 | 0.16 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.06 | 0.01 | 0.36 | 0.08 | 0.03 | 0.03 | 0.12 | 0.01 | 0.34 | 0.04 | 0.12 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.07 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.02 | 0.00 |
| FGF2 | ENSG00000138685 | 0.01 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.07 | 0.04 | 0.08 | 0.00 | 0.00 | 0.00 | 0.03 | 0.02 | 0.04 | 0.04 | 0.06 | 0.02 | 0.03 | 0.01 | 0.05 | 0.02 | 0.06 | 0.01 | 0.04 | 0.02 | 0.02 | 0.00 | 0.02 | 0.04 | 0.06 | 0.00 | 0.11 | 0.11 | 0.05 | 0.00 | 0.01 | 0.00 | 0.00 | 0.06 | 0.05 | 0.05 | 0.25 | 0.01 | 0.04 | 0.01 | 0.04 | 0.04 | 0.07 | 0.05 | 0.07 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.05 | 0.01 | 0.04 | 0.01 | 0.01 | 0.00 | 0.00 | 0.02 | 0.03 |
| MUC5B | ENSG00000117983 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.03 | 0.01 | 0.02 | 0.01 | 0.11 | 0.00 | 0.00 | 0.02 | 0.05 | 0.03 | 0.07 | 0.01 | 0.16 | 0.02 | 0.07 | 0.05 | 0.14 | 0.02 | 0.06 | 0.02 | 0.02 | 0.01 | 0.03 | 0.01 | 0.06 | 0.04 | 0.03 | 0.03 | 0.01 | 0.05 | 0.06 | 0.02 | 0.06 | 0.00 | 0.00 | 0.03 | 0.12 | 0.03 | 0.48 | 0.01 | 0.07 | 0.04 | 0.09 | 0.03 | 0.09 | 0.07 | 0.20 | 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 | 0.04 |
| THOP1 | ENSG00000172009 | 0.00 | 0.01 | 0.00 | 0.02 | 0.00 | 0.02 | 0.01 | 0.06 | 0.04 | 0.13 | 0.02 | 0.00 | 0.03 | 0.10 | 0.01 | 0.09 | 0.02 | 0.12 | 0.02 | 0.13 | 0.05 | 0.15 | 0.01 | 0.10 | 0.01 | 0.05 | 0.01 | 0.10 | 0.00 | 0.07 | 0.02 | 0.13 | 0.00 | 0.03 | 0.03 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.04 | 0.14 | 0.03 | 0.90 | 0.09 | 0.18 | 0.00 | 0.27 | 0.07 | 0.75 | 0.15 | 0.14 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.03 | 0.02 | 0.02 | 0.06 | 0.01 | 0.01 | 0.02 | 0.02 | 0.06 |
| LGR6 | ENSG00000133067 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.04 | 0.08 | 0.02 | 0.00 | 0.10 | 0.00 | 0.13 | 0.00 | 0.08 | 0.01 | 0.06 | 0.01 | 0.15 | 0.06 | 0.08 | 0.02 | 0.04 | 0.01 | 0.06 | 0.04 | 0.01 | 0.00 | 0.19 | 0.01 | 0.18 | 0.02 | 0.04 | 0.04 | 0.01 | 0.00 | 0.00 | 0.00 | 0.25 | 0.01 | 0.32 | 0.07 | 0.06 | 0.00 | 0.14 | 0.01 | 0.25 | 0.00 | 0.13 | 0.12 | 0.08 | 0.00 | 0.01 | 0.00 | 0.26 | 0.02 | 0.00 | 0.01 | 0.05 | 0.01 | 0.09 | 0.00 | 0.20 | 0.01 |
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