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 |
| SCNN1D | ENSG00000162572 | 0.00 | 0.05 | 0.01 | 0.10 | 0.00 | 0.00 | 0.02 | 0.03 | 0.10 | 0.08 | 0.00 | 0.02 | 0.04 | 0.27 | 0.09 | 0.06 | 0.08 | 0.11 | 0.06 | 0.09 | 0.13 | 0.08 | 0.09 | 0.09 | 0.02 | 0.11 | 0.00 | 0.17 | 0.05 | 0.05 | 0.02 | 0.31 | 0.00 | 1.01 | 0.05 | 0.17 | 0.01 | 0.12 | 0.00 | 0.00 | 0.04 | 0.19 | 0.23 | 0.38 | 0.06 | 0.11 | 0.05 | 0.12 | 0.08 | 0.27 | 0.18 | 0.28 | 0.10 | 0.12 | 0.02 | 0.00 | 0.00 | 0.19 | 0.00 | 0.03 | 0.03 | 0.15 | 0.00 | 0.14 | 0.07 | 0.13 |
| PTPRB | ENSG00000127329 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.03 | 0.00 | 0.29 | 0.03 | 0.00 | 0.00 | 0.03 | 0.00 | 0.25 | 0.01 | 0.24 | 0.01 | 0.21 | 0.02 | 0.35 | 0.01 | 0.30 | 0.02 | 0.00 | 0.01 | 0.04 | 0.04 | 0.13 | 0.02 | 0.02 | 0.00 | 0.06 | 0.01 | 0.30 | 0.02 | 0.05 | 0.02 | 0.00 | 0.00 | 0.26 | 0.02 | 0.29 | 0.05 | 0.07 | 0.01 | 0.03 | 0.01 | 0.56 | 0.07 | 1.04 | 0.05 | 0.28 | 0.00 | 0.00 | 0.00 | 0.11 | 0.00 | 0.04 | 0.02 | 0.15 | 0.04 | 0.02 | 0.00 | 0.24 | 0.02 |
| ULK2 | ENSG00000083290 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.02 | 0.15 | 0.07 | 0.02 | 0.01 | 0.00 | 0.02 | 0.08 | 0.04 | 0.10 | 0.05 | 0.03 | 0.03 | 0.06 | 0.08 | 0.04 | 0.05 | 0.02 | 0.03 | 0.01 | 0.06 | 0.08 | 0.01 | 0.10 | 0.04 | 0.09 | 0.01 | 0.07 | 0.04 | 0.01 | 0.01 | 0.00 | 0.00 | 0.12 | 0.05 | 0.05 | 0.14 | 0.02 | 0.05 | 0.07 | 0.07 | 0.33 | 0.21 | 0.69 | 0.03 | 0.03 | 0.00 | 0.00 | 0.00 | 0.06 | 0.00 | 0.01 | 0.01 | 0.01 | 0.03 | 0.00 | 0.00 | 0.02 | 0.03 |
| SLC1A1 | ENSG00000106688 | 0.02 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.06 | 0.14 | 0.11 | 0.01 | 0.01 | 0.04 | 0.06 | 0.05 | 0.11 | 0.13 | 0.10 | 0.21 | 0.06 | 0.12 | 0.13 | 0.12 | 0.09 | 0.01 | 0.02 | 0.04 | 0.05 | 0.01 | 0.07 | 0.07 | 0.03 | 0.03 | 0.01 | 0.12 | 0.03 | 0.00 | 0.03 | 0.00 | 0.00 | 0.09 | 0.06 | 0.19 | 0.19 | 0.21 | 0.04 | 0.09 | 0.02 | 0.07 | 0.15 | 0.22 | 0.12 | 0.01 | 0.10 | 0.00 | 0.00 | 0.07 | 0.02 | 0.00 | 0.08 | 0.01 | 0.19 | 0.00 | 0.00 | 0.10 | 0.11 |
| LIMK2 | ENSG00000182541 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.02 | 0.00 | 0.04 | 0.20 | 0.01 | 0.02 | 0.03 | 0.00 | 0.00 | 0.05 | 0.02 | 0.18 | 0.01 | 0.02 | 0.00 | 0.04 | 0.01 | 0.01 | 0.02 | 0.02 | 0.01 | 0.01 | 0.01 | 0.01 | 0.02 | 0.02 | 0.01 | 0.00 | 0.05 | 0.01 | 0.08 | 0.01 | 0.01 | 0.00 | 0.00 | 0.04 | 0.02 | 0.25 | 0.05 | 0.05 | 0.00 | 0.12 | 0.01 | 0.18 | 0.02 | 0.04 | 0.03 | 0.08 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.01 | 0.04 | 0.00 | 0.00 | 0.03 | 0.05 |
| GLUL | ENSG00000135821 | 0.02 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.03 | 0.21 | 0.02 | 0.02 | 0.00 | 0.10 | 0.03 | 0.10 | 0.01 | 0.14 | 0.01 | 0.03 | 0.01 | 0.15 | 0.02 | 0.10 | 0.00 | 0.03 | 0.00 | 0.12 | 0.00 | 0.04 | 0.00 | 0.15 | 0.01 | 0.17 | 0.01 | 0.02 | 0.04 | 0.02 | 0.00 | 0.01 | 0.00 | 0.16 | 0.01 | 0.34 | 0.03 | 0.08 | 0.01 | 0.07 | 0.00 | 0.27 | 0.00 | 0.22 | 0.03 | 0.07 | 0.00 | 0.01 | 0.00 | 0.30 | 0.02 | 0.01 | 0.00 | 0.02 | 0.01 | 0.02 | 0.00 | 0.14 | 0.02 |
| EPHA3 | ENSG00000044524 | 0.00 | 0.03 | 0.01 | 0.01 | 0.00 | 0.03 | 0.02 | 0.04 | 0.11 | 0.08 | 0.00 | 0.00 | 0.02 | 0.08 | 0.08 | 0.05 | 0.15 | 0.15 | 0.05 | 0.09 | 0.11 | 0.14 | 0.05 | 0.04 | 0.02 | 0.02 | 0.02 | 0.01 | 0.01 | 0.01 | 0.03 | 0.03 | 0.18 | 0.06 | 0.07 | 0.04 | 0.00 | 0.04 | 0.00 | 0.00 | 0.06 | 0.05 | 0.15 | 0.06 | 0.08 | 0.13 | 0.05 | 0.05 | 0.10 | 0.28 | 0.36 | 0.07 | 0.05 | 0.00 | 0.00 | 0.01 | 0.02 | 0.00 | 0.00 | 0.02 | 0.00 | 0.03 | 0.00 | 0.00 | 0.08 | 0.01 |
| NPY1R | ENSG00000164128 | 0.00 | 0.02 | 0.00 | 0.02 | 0.06 | 0.02 | 0.04 | 0.02 | 0.04 | 0.13 | 0.00 | 0.01 | 0.00 | 0.02 | 0.01 | 0.08 | 0.02 | 0.13 | 0.01 | 0.10 | 0.09 | 0.08 | 0.05 | 0.10 | 0.02 | 0.06 | 0.02 | 0.04 | 0.00 | 0.03 | 0.05 | 0.09 | 0.00 | 0.15 | 0.10 | 0.07 | 0.00 | 0.03 | 0.00 | 0.00 | 0.05 | 0.07 | 0.08 | 0.28 | 0.04 | 0.08 | 0.00 | 0.05 | 0.14 | 0.05 | 0.08 | 0.17 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.03 | 0.00 | 0.11 | 0.00 | 0.04 | 0.00 | 0.00 | 0.05 | 0.05 |
| KCNQ1 | ENSG00000053918 | 0.01 | 0.00 | 0.01 | 0.00 | 0.01 | 0.03 | 0.01 | 0.02 | 0.01 | 0.11 | 0.00 | 0.00 | 0.02 | 0.05 | 0.02 | 0.07 | 0.01 | 0.17 | 0.02 | 0.07 | 0.02 | 0.16 | 0.02 | 0.09 | 0.04 | 0.02 | 0.01 | 0.04 | 0.01 | 0.06 | 0.04 | 0.03 | 0.03 | 0.01 | 0.06 | 0.08 | 0.02 | 0.07 | 0.00 | 0.00 | 0.03 | 0.12 | 0.03 | 0.47 | 0.02 | 0.07 | 0.04 | 0.08 | 0.08 | 0.09 | 0.08 | 0.15 | 0.02 | 0.04 | 0.00 | 0.00 | 0.05 | 0.00 | 0.01 | 0.11 | 0.01 | 0.06 | 0.00 | 0.00 | 0.01 | 0.05 |
| SLC38A10 | ENSG00000157637 | 0.02 | 0.00 | 0.05 | 0.00 | 0.02 | 0.00 | 0.03 | 0.03 | 0.21 | 0.00 | 0.00 | 0.00 | 0.09 | 0.03 | 0.17 | 0.02 | 0.19 | 0.05 | 0.06 | 0.06 | 0.13 | 0.09 | 0.13 | 0.04 | 0.06 | 0.00 | 0.06 | 0.03 | 0.02 | 0.09 | 0.33 | 0.02 | 0.15 | 0.01 | 0.17 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.33 | 0.04 | 0.40 | 0.05 | 0.10 | 0.09 | 0.15 | 0.01 | 0.67 | 0.07 | 0.19 | 0.06 | 0.06 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.01 | 0.04 | 0.01 | 0.14 | 0.00 | 0.25 | 0.01 |
| GBA2 | ENSG00000070610 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.12 | 0.03 | 0.00 | 0.00 | 0.01 | 0.09 | 0.07 | 0.03 | 0.39 | 0.04 | 0.29 | 0.03 | 0.27 | 0.03 | 0.18 | 0.02 | 0.02 | 0.00 | 0.02 | 0.00 | 0.19 | 0.00 | 0.03 | 0.02 | 0.19 | 0.01 | 0.16 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.08 | 0.02 | 0.12 | 0.06 | 0.02 | 0.01 | 0.07 | 0.01 | 0.02 | 0.13 | 0.13 | 0.05 | 0.03 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.06 | 0.06 | 0.00 | 0.03 | 0.09 | 0.05 |
| PPP3CA | ENSG00000138814 | 0.00 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.03 | 0.03 | 0.06 | 0.00 | 0.00 | 0.00 | 0.05 | 0.02 | 0.03 | 0.03 | 0.05 | 0.01 | 0.02 | 0.02 | 0.08 | 0.02 | 0.03 | 0.01 | 0.03 | 0.01 | 0.05 | 0.00 | 0.02 | 0.01 | 0.13 | 0.00 | 0.03 | 0.04 | 0.02 | 0.02 | 0.01 | 0.00 | 0.00 | 0.04 | 0.05 | 0.02 | 0.30 | 0.01 | 0.02 | 0.02 | 0.04 | 0.00 | 0.14 | 0.04 | 0.06 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.05 | 0.00 | 0.02 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.04 |
| CCDC101 | ENSG00000176476 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.18 | 0.01 | 0.00 | 0.00 | 0.03 | 0.00 | 0.07 | 0.01 | 0.10 | 0.01 | 0.03 | 0.01 | 0.06 | 0.00 | 0.06 | 0.00 | 0.03 | 0.01 | 0.01 | 0.00 | 0.01 | 0.00 | 0.06 | 0.01 | 0.00 | 0.01 | 0.08 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.00 | 0.07 | 0.03 | 0.02 | 0.02 | 0.08 | 0.00 | 0.35 | 0.03 | 0.06 | 0.02 | 0.00 | 0.01 | 0.00 | 0.01 | 0.06 | 0.00 | 0.00 | 0.02 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.01 |
| TUBB6 | ENSG00000176014 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.05 | 0.02 | 0.00 | 0.00 | 0.00 | 0.02 | 0.05 | 0.01 | 0.05 | 0.02 | 0.02 | 0.01 | 0.04 | 0.03 | 0.06 | 0.02 | 0.01 | 0.02 | 0.03 | 0.01 | 0.02 | 0.01 | 0.01 | 0.00 | 0.00 | 0.08 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.02 | 0.06 | 0.05 | 0.01 | 0.02 | 0.02 | 0.00 | 0.06 | 0.00 | 0.07 | 0.03 | 0.02 | 0.02 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 |
| LOXL4 | ENSG00000138131 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.11 | 0.01 | 0.10 | 0.00 | 0.02 | 0.00 | 0.16 | 0.01 | 0.03 | 0.02 | 0.08 | 0.00 | 0.05 | 0.02 | 0.09 | 0.01 | 0.10 | 0.01 | 0.10 | 0.00 | 0.06 | 0.01 | 0.03 | 0.02 | 0.06 | 0.16 | 0.14 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.01 | 0.02 | 0.08 | 0.07 | 0.34 | 0.01 | 0.07 | 0.02 | 0.09 | 0.03 | 0.09 | 0.02 | 0.05 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.07 | 0.00 | 0.04 | 0.00 | 0.05 | 0.00 | 0.00 | 0.01 | 0.04 |
| ITGA1 | ENSG00000213949 | 0.00 | 0.00 | 0.00 | 0.01 | 0.03 | 0.00 | 0.01 | 0.15 | 0.06 | 0.11 | 0.00 | 0.00 | 0.01 | 0.01 | 0.07 | 0.06 | 0.05 | 0.09 | 0.02 | 0.08 | 0.04 | 0.14 | 0.04 | 0.09 | 0.03 | 0.04 | 0.02 | 0.03 | 0.00 | 0.05 | 0.02 | 0.01 | 0.00 | 0.10 | 0.09 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.03 | 0.08 | 0.10 | 0.39 | 0.04 | 0.08 | 0.03 | 0.11 | 0.04 | 0.27 | 0.09 | 0.05 | 0.00 | 0.02 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.03 | 0.02 |
| AADAT | ENSG00000109576 | 0.00 | 0.03 | 0.00 | 0.02 | 0.06 | 0.02 | 0.03 | 0.03 | 0.06 | 0.15 | 0.00 | 0.00 | 0.00 | 0.02 | 0.02 | 0.09 | 0.02 | 0.18 | 0.02 | 0.09 | 0.07 | 0.10 | 0.05 | 0.13 | 0.03 | 0.07 | 0.02 | 0.06 | 0.00 | 0.05 | 0.06 | 0.11 | 0.00 | 0.17 | 0.10 | 0.11 | 0.00 | 0.03 | 0.00 | 0.00 | 0.05 | 0.08 | 0.09 | 0.31 | 0.05 | 0.09 | 0.02 | 0.06 | 0.09 | 0.10 | 0.08 | 0.19 | 0.01 | 0.00 | 0.00 | 0.00 | 0.09 | 0.09 | 0.01 | 0.11 | 0.00 | 0.06 | 0.00 | 0.00 | 0.03 | 0.05 |
| HSD17B4 | ENSG00000133835 | 0.23 | 0.01 | 0.03 | 0.01 | 0.00 | 0.00 | 0.03 | 0.10 | 0.03 | 0.07 | 0.00 | 0.01 | 0.00 | 0.08 | 0.02 | 0.08 | 0.00 | 0.07 | 0.01 | 0.05 | 0.03 | 0.07 | 0.02 | 0.12 | 0.01 | 0.11 | 0.01 | 0.07 | 0.00 | 0.03 | 0.07 | 0.04 | 0.05 | 0.02 | 0.23 | 0.05 | 0.00 | 0.03 | 0.00 | 0.00 | 0.02 | 0.05 | 0.11 | 0.30 | 0.02 | 0.04 | 0.01 | 0.03 | 0.06 | 0.08 | 0.06 | 0.03 | 0.02 | 0.00 | 0.00 | 0.09 | 0.04 | 0.02 | 0.00 | 0.02 | 0.00 | 0.01 | 0.00 | 0.03 | 0.04 | 0.08 |
| BAZ1A | ENSG00000198604 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.04 | 0.06 | 0.00 | 0.01 | 0.00 | 0.02 | 0.60 | 0.01 | 0.13 | 0.05 | 0.07 | 0.03 | 0.17 | 0.03 | 0.08 | 0.02 | 0.03 | 0.01 | 0.02 | 0.03 | 0.01 | 0.01 | 0.06 | 0.04 | 0.05 | 0.02 | 0.11 | 0.03 | 0.00 | 0.02 | 0.00 | 0.00 | 0.16 | 0.02 | 0.15 | 0.11 | 0.07 | 0.00 | 0.05 | 0.02 | 0.10 | 0.03 | 0.22 | 0.05 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.01 | 0.08 | 0.00 | 0.00 | 0.02 | 0.01 |
| SMYD4 | ENSG00000186532 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.06 | 0.05 | 0.05 | 0.00 | 0.00 | 0.01 | 0.02 | 0.01 | 0.08 | 0.03 | 0.03 | 0.01 | 0.04 | 0.06 | 0.06 | 0.03 | 0.03 | 0.04 | 0.01 | 0.01 | 0.00 | 0.00 | 0.03 | 0.04 | 0.13 | 0.00 | 0.03 | 0.06 | 0.03 | 0.00 | 0.04 | 0.00 | 0.00 | 0.02 | 0.06 | 0.15 | 0.11 | 0.02 | 0.03 | 0.07 | 0.05 | 0.16 | 0.14 | 0.18 | 0.22 | 0.01 | 0.02 | 0.00 | 0.02 | 0.00 | 0.06 | 0.01 | 0.00 | 0.01 | 0.04 | 0.00 | 0.00 | 0.02 | 0.06 |
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