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 |
| AXIN2 | ENSG00000168646 | 0.02 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.03 | 0.02 | 0.25 | 0.00 | 0.02 | 0.00 | 0.12 | 0.00 | 0.14 | 0.01 | 0.18 | 0.01 | 0.07 | 0.02 | 0.21 | 0.04 | 0.13 | 0.03 | 0.09 | 0.01 | 0.12 | 0.05 | 0.05 | 0.10 | 0.18 | 0.01 | 0.12 | 0.01 | 0.15 | 0.03 | 0.02 | 0.00 | 0.00 | 0.00 | 0.49 | 0.02 | 0.23 | 0.05 | 0.17 | 0.02 | 0.09 | 0.03 | 0.45 | 0.02 | 0.20 | 0.03 | 0.01 | 0.00 | 0.00 | 0.00 | 0.05 | 0.10 | 0.07 | 0.00 | 0.03 | 0.00 | 0.17 | 0.00 | 0.23 | 0.01 |
| KCNK5 | ENSG00000164626 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.12 | 0.02 | 0.01 | 0.00 | 0.02 | 0.02 | 0.10 | 0.01 | 0.09 | 0.04 | 0.04 | 0.02 | 0.26 | 0.03 | 0.13 | 0.02 | 0.05 | 0.01 | 0.07 | 0.00 | 0.03 | 0.01 | 0.05 | 0.02 | 0.05 | 0.03 | 0.03 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.10 | 0.03 | 0.30 | 0.05 | 0.05 | 0.01 | 0.04 | 0.01 | 0.09 | 0.03 | 0.11 | 0.05 | 0.05 | 0.01 | 0.00 | 0.00 | 0.14 | 0.00 | 0.02 | 0.00 | 0.02 | 0.01 | 0.09 | 0.00 | 0.05 | 0.00 |
| SLC7A1 | ENSG00000139514 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.05 | 0.16 | 0.04 | 0.00 | 0.02 | 0.00 | 0.18 | 0.02 | 0.09 | 0.03 | 0.11 | 0.02 | 0.14 | 0.11 | 0.06 | 0.10 | 0.04 | 0.17 | 0.00 | 0.35 | 0.02 | 0.01 | 0.01 | 0.03 | 0.15 | 0.00 | 0.15 | 0.00 | 0.09 | 0.00 | 0.00 | 0.00 | 0.01 | 0.12 | 0.06 | 0.08 | 0.17 | 0.03 | 0.14 | 0.01 | 0.06 | 0.01 | 0.12 | 0.10 | 0.26 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.09 | 0.02 | 0.05 | 0.00 | 0.07 | 0.00 | 0.00 | 0.07 | 0.03 |
| CD1C | ENSG00000158481 | 0.03 | 0.00 | 0.01 | 0.01 | 0.00 | 0.03 | 0.02 | 0.05 | 0.38 | 0.01 | 0.02 | 0.00 | 0.11 | 0.00 | 0.27 | 0.00 | 0.25 | 0.00 | 0.06 | 0.00 | 0.25 | 0.00 | 0.13 | 0.00 | 0.03 | 0.00 | 0.11 | 0.00 | 0.07 | 0.00 | 0.29 | 0.00 | 0.41 | 0.01 | 0.16 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.27 | 0.01 | 0.38 | 0.02 | 0.15 | 0.00 | 0.14 | 0.00 | 0.29 | 0.00 | 0.38 | 0.02 | 0.11 | 0.00 | 0.00 | 0.00 | 0.25 | 0.00 | 0.01 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.17 | 0.01 |
| MMEL1 | ENSG00000142606 | 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 |
| CHRNB4 | ENSG00000117971 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.02 | 0.00 | 0.02 | 0.03 | 0.03 | 0.00 | 0.00 | 0.09 | 0.00 | 0.03 | 0.01 | 0.09 | 0.01 | 0.03 | 0.02 | 0.07 | 0.03 | 0.06 | 0.03 | 0.03 | 0.01 | 0.03 | 0.00 | 0.04 | 0.01 | 0.04 | 0.03 | 0.05 | 0.01 | 0.06 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.10 | 0.03 | 0.18 | 0.12 | 0.13 | 0.01 | 0.03 | 0.03 | 0.13 | 0.07 | 0.06 | 0.07 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.00 | 0.01 | 0.01 | 0.01 | 0.02 | 0.00 | 0.00 | 0.15 | 0.01 |
| ABAT | ENSG00000183044 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.28 | 0.05 | 0.00 | 0.00 | 0.06 | 0.00 | 0.05 | 0.02 | 0.06 | 0.05 | 0.05 | 0.01 | 0.07 | 0.05 | 0.06 | 0.04 | 0.00 | 0.02 | 0.00 | 0.02 | 0.01 | 0.00 | 0.02 | 0.01 | 0.00 | 0.05 | 0.08 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.07 | 0.02 | 0.15 | 0.15 | 0.16 | 0.02 | 0.03 | 0.02 | 0.09 | 0.05 | 0.14 | 0.02 | 0.02 | 0.00 | 0.00 | 0.00 | 0.05 | 0.00 | 0.01 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.04 | 0.01 |
| FNTA | ENSG00000168522 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.04 | 0.05 | 0.18 | 0.08 | 0.00 | 0.00 | 0.04 | 0.02 | 0.17 | 0.06 | 0.35 | 0.04 | 0.13 | 0.03 | 0.34 | 0.08 | 0.08 | 0.05 | 0.14 | 0.05 | 0.07 | 0.06 | 0.03 | 0.01 | 0.04 | 0.05 | 0.00 | 0.02 | 0.09 | 0.01 | 0.01 | 0.02 | 0.00 | 0.00 | 0.30 | 0.07 | 0.30 | 0.05 | 0.07 | 0.04 | 0.17 | 0.02 | 1.02 | 0.08 | 0.12 | 0.07 | 0.02 | 0.00 | 0.01 | 0.00 | 0.03 | 0.03 | 0.01 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.07 | 0.02 |
| SERPINH1 | ENSG00000149257 | 0.00 | 0.01 | 0.00 | 0.00 | 0.10 | 0.00 | 0.04 | 0.00 | 0.16 | 0.03 | 0.00 | 0.00 | 0.08 | 0.00 | 0.13 | 0.01 | 0.14 | 0.02 | 0.24 | 0.03 | 0.43 | 0.01 | 0.14 | 0.01 | 0.02 | 0.00 | 0.02 | 0.01 | 0.01 | 0.01 | 0.06 | 0.01 | 0.02 | 0.02 | 0.03 | 0.00 | 0.02 | 0.02 | 0.00 | 0.00 | 0.43 | 0.06 | 0.57 | 0.02 | 0.11 | 0.01 | 0.11 | 0.01 | 0.23 | 0.13 | 0.18 | 0.04 | 0.02 | 0.03 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.00 | 0.01 | 0.02 | 0.00 | 0.00 | 0.23 | 0.01 |
| COL5A1 | ENSG00000130635 | 0.00 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.04 | 0.01 | 0.04 | 0.03 | 0.00 | 0.01 | 0.00 | 0.02 | 0.05 | 0.03 | 0.07 | 0.02 | 0.07 | 0.03 | 0.12 | 0.02 | 0.11 | 0.02 | 0.03 | 0.01 | 0.07 | 0.04 | 0.01 | 0.00 | 0.07 | 0.04 | 0.06 | 0.01 | 0.19 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.05 | 0.07 | 0.08 | 0.25 | 0.06 | 0.02 | 0.02 | 0.05 | 0.11 | 0.14 | 0.07 | 0.15 | 0.03 | 0.03 | 0.01 | 0.00 | 0.05 | 0.00 | 0.02 | 0.01 | 0.03 | 0.04 | 0.00 | 0.00 | 0.03 | 0.02 |
| NFKB2 | ENSG00000077150 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.10 | 0.01 | 0.09 | 0.00 | 0.02 | 0.00 | 0.18 | 0.01 | 0.03 | 0.02 | 0.07 | 0.00 | 0.05 | 0.03 | 0.08 | 0.03 | 0.08 | 0.00 | 0.10 | 0.00 | 0.07 | 0.01 | 0.03 | 0.02 | 0.07 | 0.11 | 0.14 | 0.05 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.03 | 0.08 | 0.08 | 0.31 | 0.01 | 0.07 | 0.03 | 0.08 | 0.05 | 0.11 | 0.03 | 0.05 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.07 | 0.00 | 0.04 | 0.00 | 0.04 | 0.00 | 0.00 | 0.01 | 0.04 |
| POLA1 | ENSG00000101868 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.04 | 0.00 | 0.07 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.04 | 0.10 | 0.04 | 0.03 | 0.02 | 0.12 | 0.04 | 0.07 | 0.01 | 0.00 | 0.01 | 0.11 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.06 | 0.01 | 0.02 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.06 | 0.02 | 0.07 | 0.16 | 0.08 | 0.00 | 0.03 | 0.02 | 0.11 | 0.11 | 0.20 | 0.04 | 0.05 | 0.00 | 0.00 | 0.00 | 0.09 | 0.02 | 0.01 | 0.02 | 0.02 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 |
| CACNG8 | ENSG00000142408 | 0.01 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.03 | 0.00 | 0.17 | 0.03 | 0.00 | 0.00 | 0.01 | 0.07 | 0.02 | 0.06 | 0.11 | 0.09 | 0.03 | 0.02 | 0.10 | 0.03 | 0.10 | 0.03 | 0.02 | 0.02 | 0.01 | 0.04 | 0.03 | 0.04 | 0.06 | 0.02 | 0.00 | 0.07 | 0.21 | 0.00 | 0.00 | 0.03 | 0.00 | 0.00 | 0.16 | 0.03 | 0.13 | 0.27 | 0.13 | 0.06 | 0.05 | 0.06 | 0.35 | 0.10 | 0.08 | 0.18 | 0.00 | 0.06 | 0.01 | 0.00 | 0.13 | 0.03 | 0.01 | 0.17 | 0.02 | 0.12 | 0.00 | 0.00 | 0.04 | 0.03 |
| ITGA4 | ENSG00000115232 | 0.02 | 0.01 | 0.08 | 0.00 | 0.00 | 0.00 | 0.01 | 0.07 | 0.07 | 0.05 | 0.00 | 0.00 | 0.00 | 0.03 | 0.05 | 0.01 | 0.16 | 0.03 | 0.13 | 0.01 | 0.12 | 0.03 | 0.05 | 0.05 | 0.01 | 0.01 | 0.02 | 0.02 | 0.03 | 0.01 | 0.04 | 0.03 | 0.00 | 0.05 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.03 | 0.38 | 0.05 | 0.12 | 0.02 | 0.06 | 0.01 | 0.07 | 0.00 | 0.02 | 0.09 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.03 |
| PKM | ENSG00000067225 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.02 | 0.01 | 0.02 | 0.05 | 0.02 | 0.00 | 0.00 | 0.09 | 0.02 | 0.04 | 0.01 | 0.06 | 0.01 | 0.04 | 0.02 | 0.07 | 0.02 | 0.08 | 0.02 | 0.03 | 0.00 | 0.01 | 0.03 | 0.03 | 0.01 | 0.02 | 0.02 | 0.00 | 0.01 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.09 | 0.03 | 0.24 | 0.10 | 0.10 | 0.01 | 0.06 | 0.04 | 0.13 | 0.01 | 0.07 | 0.08 | 0.01 | 0.01 | 0.00 | 0.00 | 0.06 | 0.00 | 0.01 | 0.01 | 0.02 | 0.01 | 0.00 | 0.00 | 0.12 | 0.00 |
| WNT2 | ENSG00000105989 | 0.02 | 0.01 | 0.11 | 0.00 | 0.01 | 0.00 | 0.01 | 0.04 | 0.08 | 0.03 | 0.00 | 0.01 | 0.03 | 0.03 | 0.14 | 0.03 | 0.13 | 0.05 | 0.07 | 0.07 | 0.18 | 0.16 | 0.19 | 0.06 | 0.01 | 0.00 | 0.00 | 0.03 | 0.01 | 0.03 | 0.13 | 0.03 | 0.00 | 0.02 | 0.02 | 0.06 | 0.00 | 0.02 | 0.00 | 0.00 | 0.06 | 0.03 | 0.31 | 0.07 | 0.04 | 0.05 | 0.05 | 0.03 | 0.15 | 0.08 | 0.11 | 0.03 | 0.03 | 0.02 | 0.00 | 0.03 | 0.09 | 0.04 | 0.10 | 0.00 | 0.06 | 0.00 | 0.00 | 0.00 | 0.14 | 0.02 |
| CHRNA3 | ENSG00000080644 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.02 | 0.00 | 0.02 | 0.03 | 0.03 | 0.00 | 0.00 | 0.09 | 0.00 | 0.03 | 0.01 | 0.09 | 0.01 | 0.03 | 0.02 | 0.07 | 0.03 | 0.06 | 0.03 | 0.03 | 0.01 | 0.03 | 0.00 | 0.04 | 0.01 | 0.04 | 0.03 | 0.05 | 0.01 | 0.06 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.10 | 0.03 | 0.18 | 0.12 | 0.12 | 0.01 | 0.03 | 0.03 | 0.13 | 0.07 | 0.06 | 0.07 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.00 | 0.01 | 0.01 | 0.01 | 0.02 | 0.00 | 0.00 | 0.14 | 0.01 |
| ITGB5 | ENSG00000082781 | 0.00 | 0.01 | 0.00 | 0.00 | 0.05 | 0.00 | 0.04 | 0.04 | 0.05 | 0.02 | 0.00 | 0.01 | 0.00 | 0.01 | 0.04 | 0.02 | 0.11 | 0.01 | 0.04 | 0.00 | 0.10 | 0.07 | 0.06 | 0.02 | 0.00 | 0.00 | 0.03 | 0.01 | 0.00 | 0.00 | 0.03 | 0.01 | 0.00 | 0.05 | 0.03 | 0.01 | 0.00 | 0.05 | 0.00 | 0.00 | 0.03 | 0.04 | 0.26 | 0.05 | 0.08 | 0.01 | 0.06 | 0.01 | 0.11 | 0.08 | 0.10 | 0.06 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.02 | 0.01 | 0.06 | 0.00 | 0.00 | 0.00 | 0.04 |
| CA14 | ENSG00000118298 | 0.03 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.07 | 0.00 | 0.54 | 0.01 | 0.02 | 0.00 | 0.11 | 0.02 | 0.43 | 0.00 | 0.31 | 0.00 | 0.09 | 0.01 | 0.23 | 0.00 | 0.22 | 0.00 | 0.03 | 0.00 | 0.17 | 0.00 | 0.06 | 0.00 | 0.37 | 0.00 | 0.43 | 0.01 | 0.24 | 0.00 | 0.11 | 0.00 | 0.00 | 0.00 | 0.42 | 0.01 | 0.68 | 0.02 | 0.19 | 0.00 | 0.28 | 0.00 | 0.54 | 0.00 | 0.43 | 0.02 | 0.14 | 0.00 | 0.00 | 0.00 | 0.28 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.21 | 0.00 |
| ASH2L | ENSG00000129691 | 0.00 | 0.01 | 0.03 | 0.00 | 0.00 | 0.00 | 0.07 | 0.07 | 0.40 | 0.04 | 0.00 | 0.00 | 0.04 | 0.00 | 0.17 | 0.04 | 0.94 | 0.03 | 0.31 | 0.03 | 0.37 | 0.06 | 0.08 | 0.03 | 0.16 | 0.04 | 0.11 | 0.04 | 0.10 | 0.00 | 0.05 | 0.05 | 0.02 | 0.02 | 0.05 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.75 | 0.04 | 0.23 | 0.09 | 0.05 | 0.02 | 0.13 | 0.06 | 0.64 | 0.11 | 0.25 | 0.04 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.02 | 0.00 | 0.01 | 0.04 | 0.03 |
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