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 |
| HSD3B7 | ENSG00000099377 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.09 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.11 | 0.01 | 0.11 | 0.01 | 0.03 | 0.02 | 0.08 | 0.00 | 0.07 | 0.00 | 0.07 | 0.00 | 0.10 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.10 | 0.01 | 0.09 | 0.03 | 0.02 | 0.03 | 0.14 | 0.00 | 0.60 | 0.05 | 0.06 | 0.02 | 0.02 | 0.01 | 0.00 | 0.02 | 0.05 | 0.02 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 |
| SETD1A | ENSG00000099381 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.09 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.11 | 0.01 | 0.11 | 0.01 | 0.03 | 0.02 | 0.10 | 0.00 | 0.07 | 0.00 | 0.07 | 0.00 | 0.10 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.10 | 0.01 | 0.10 | 0.03 | 0.02 | 0.03 | 0.14 | 0.00 | 0.62 | 0.05 | 0.06 | 0.02 | 0.02 | 0.01 | 0.00 | 0.02 | 0.05 | 0.02 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 |
| AMELY | ENSG00000099721 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |
| PRKY | ENSG00000099725 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |
| IGFALS | ENSG00000099769 | 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 | 0.04 | 0.03 | 0.02 | 0.02 | 0.04 | 0.03 | 0.00 | 0.05 | 0.18 | 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 |
| MADCAM1 | ENSG00000099866 | 0.00 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.02 | 0.02 | 0.14 | 0.05 | 0.00 | 0.03 | 0.09 | 0.03 | 0.09 | 0.03 | 0.15 | 0.01 | 0.16 | 0.05 | 0.18 | 0.04 | 0.07 | 0.01 | 0.06 | 0.01 | 0.09 | 0.01 | 0.07 | 0.03 | 0.13 | 0.04 | 0.03 | 0.13 | 0.01 | 0.03 | 0.01 | 0.00 | 0.01 | 0.02 | 0.17 | 0.03 | 0.91 | 0.05 | 0.22 | 0.03 | 0.25 | 0.00 | 0.84 | 0.25 | 0.23 | 0.01 | 0.01 | 0.00 | 0.02 | 0.03 | 0.00 | 0.05 | 0.02 | 0.08 | 0.01 | 0.01 | 0.03 | 0.03 | 0.08 |
| CECR2 | ENSG00000099954 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.04 | 0.15 | 0.06 | 0.03 | 0.00 | 0.07 | 0.05 | 0.06 | 0.04 | 0.14 | 0.08 | 0.06 | 0.04 | 0.06 | 0.13 | 0.05 | 0.04 | 0.01 | 0.02 | 0.06 | 0.03 | 0.00 | 0.02 | 0.02 | 0.04 | 0.08 | 0.10 | 0.06 | 0.07 | 0.00 | 0.01 | 0.02 | 0.00 | 0.06 | 0.06 | 0.15 | 0.10 | 0.05 | 0.01 | 0.06 | 0.05 | 0.34 | 0.09 | 0.11 | 0.06 | 0.10 | 0.04 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.01 | 0.03 | 0.00 | 0.00 | 0.10 | 0.03 |
| P2RX6 | ENSG00000099957 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.05 | 0.19 | 0.06 | 0.03 | 0.01 | 0.04 | 0.05 | 0.14 | 0.03 | 0.29 | 0.07 | 0.08 | 0.03 | 0.06 | 0.07 | 0.08 | 0.04 | 0.02 | 0.01 | 0.05 | 0.03 | 0.00 | 0.02 | 0.03 | 0.03 | 0.03 | 0.10 | 0.06 | 0.14 | 0.00 | 0.01 | 0.00 | 0.00 | 0.07 | 0.05 | 0.25 | 0.07 | 0.04 | 0.01 | 0.08 | 0.06 | 0.43 | 0.04 | 0.21 | 0.07 | 0.29 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.03 | 0.03 | 0.00 | 0.00 | 0.14 | 0.03 |
| SLC7A4 | ENSG00000099960 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.05 | 0.19 | 0.06 | 0.03 | 0.01 | 0.04 | 0.05 | 0.14 | 0.03 | 0.29 | 0.07 | 0.08 | 0.03 | 0.06 | 0.07 | 0.08 | 0.04 | 0.02 | 0.01 | 0.05 | 0.03 | 0.00 | 0.02 | 0.03 | 0.03 | 0.03 | 0.10 | 0.06 | 0.14 | 0.00 | 0.01 | 0.00 | 0.00 | 0.07 | 0.05 | 0.25 | 0.07 | 0.04 | 0.01 | 0.08 | 0.06 | 0.43 | 0.04 | 0.21 | 0.07 | 0.29 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.03 | 0.03 | 0.00 | 0.00 | 0.14 | 0.03 |
| BCL2L13 | ENSG00000099968 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.04 | 0.16 | 0.06 | 0.03 | 0.00 | 0.07 | 0.05 | 0.06 | 0.04 | 0.14 | 0.08 | 0.07 | 0.05 | 0.06 | 0.10 | 0.04 | 0.04 | 0.01 | 0.01 | 0.06 | 0.03 | 0.00 | 0.02 | 0.01 | 0.05 | 0.08 | 0.10 | 0.06 | 0.07 | 0.00 | 0.01 | 0.02 | 0.00 | 0.05 | 0.06 | 0.14 | 0.10 | 0.04 | 0.01 | 0.06 | 0.05 | 0.30 | 0.09 | 0.11 | 0.07 | 0.10 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.01 | 0.02 | 0.00 | 0.00 | 0.12 | 0.03 |
| OSM | ENSG00000099985 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.02 | 0.01 | 0.04 | 0.23 | 0.01 | 0.00 | 0.05 | 0.00 | 0.00 | 0.05 | 0.02 | 0.18 | 0.01 | 0.03 | 0.00 | 0.03 | 0.01 | 0.05 | 0.02 | 0.03 | 0.01 | 0.04 | 0.01 | 0.02 | 0.02 | 0.02 | 0.02 | 0.04 | 0.05 | 0.02 | 0.07 | 0.00 | 0.01 | 0.00 | 0.00 | 0.04 | 0.02 | 0.32 | 0.04 | 0.06 | 0.00 | 0.14 | 0.01 | 0.22 | 0.00 | 0.02 | 0.04 | 0.09 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.00 | 0.02 | 0.05 |
| GGT5 | ENSG00000099998 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.02 | 0.18 | 0.03 | 0.02 | 0.01 | 0.01 | 0.05 | 0.08 | 0.02 | 0.18 | 0.02 | 0.04 | 0.00 | 0.07 | 0.02 | 0.05 | 0.01 | 0.01 | 0.01 | 0.09 | 0.01 | 0.00 | 0.01 | 0.04 | 0.03 | 0.00 | 0.05 | 0.12 | 0.03 | 0.00 | 0.01 | 0.00 | 0.00 | 0.08 | 0.03 | 0.17 | 0.04 | 0.02 | 0.00 | 0.06 | 0.03 | 0.28 | 0.03 | 0.09 | 0.04 | 0.21 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.06 | 0.03 |
| MAPK1 | ENSG00000100030 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.02 | 0.19 | 0.04 | 0.03 | 0.01 | 0.04 | 0.05 | 0.15 | 0.03 | 0.30 | 0.03 | 0.08 | 0.01 | 0.06 | 0.02 | 0.09 | 0.02 | 0.02 | 0.01 | 0.06 | 0.05 | 0.00 | 0.03 | 0.02 | 0.03 | 0.05 | 0.05 | 0.03 | 0.06 | 0.00 | 0.01 | 0.00 | 0.00 | 0.06 | 0.03 | 0.26 | 0.05 | 0.04 | 0.00 | 0.07 | 0.04 | 0.42 | 0.04 | 0.21 | 0.05 | 0.29 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.03 | 0.03 | 0.00 | 0.00 | 0.12 | 0.01 |
| MFNG | ENSG00000100060 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.12 | 0.05 | 0.00 | 0.04 | 0.00 | 0.03 | 0.06 | 0.04 | 0.07 | 0.02 | 0.01 | 0.01 | 0.04 | 0.02 | 0.05 | 0.02 | 0.01 | 0.01 | 0.02 | 0.01 | 0.03 | 0.01 | 0.07 | 0.01 | 0.00 | 0.01 | 0.02 | 0.02 | 0.00 | 0.04 | 0.00 | 0.00 | 0.03 | 0.02 | 0.10 | 0.11 | 0.04 | 0.01 | 0.07 | 0.02 | 0.43 | 0.08 | 0.08 | 0.02 | 0.02 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.02 | 0.00 | 0.04 | 0.00 | 0.00 | 0.15 | 0.01 |
| PLA2G3 | ENSG00000100078 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.02 | 0.00 | 0.04 | 0.22 | 0.00 | 0.02 | 0.04 | 0.00 | 0.00 | 0.04 | 0.02 | 0.18 | 0.01 | 0.02 | 0.00 | 0.03 | 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 | 0.07 | 0.00 | 0.01 | 0.00 | 0.00 | 0.05 | 0.02 | 0.27 | 0.05 | 0.04 | 0.00 | 0.12 | 0.01 | 0.21 | 0.02 | 0.04 | 0.03 | 0.08 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.05 | 0.00 | 0.00 | 0.03 | 0.05 |
| LGALS1 | ENSG00000100097 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.11 | 0.05 | 0.00 | 0.04 | 0.00 | 0.03 | 0.07 | 0.04 | 0.08 | 0.02 | 0.01 | 0.01 | 0.04 | 0.02 | 0.03 | 0.02 | 0.01 | 0.01 | 0.02 | 0.01 | 0.02 | 0.01 | 0.10 | 0.01 | 0.08 | 0.01 | 0.02 | 0.00 | 0.00 | 0.04 | 0.00 | 0.00 | 0.03 | 0.02 | 0.12 | 0.10 | 0.04 | 0.01 | 0.08 | 0.02 | 0.38 | 0.08 | 0.06 | 0.02 | 0.02 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.02 | 0.01 | 0.04 | 0.00 | 0.00 | 0.17 | 0.01 |
| PIK3IP1 | ENSG00000100100 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.02 | 0.00 | 0.04 | 0.20 | 0.00 | 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 | 0.07 | 0.01 | 0.01 | 0.00 | 0.00 | 0.04 | 0.02 | 0.23 | 0.05 | 0.05 | 0.00 | 0.11 | 0.01 | 0.18 | 0.02 | 0.04 | 0.03 | 0.07 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.01 | 0.04 | 0.00 | 0.00 | 0.02 | 0.05 |
| GGTLC2 | ENSG00000100121 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.02 | 0.21 | 0.04 | 0.03 | 0.01 | 0.03 | 0.05 | 0.14 | 0.03 | 0.26 | 0.03 | 0.09 | 0.01 | 0.06 | 0.02 | 0.06 | 0.02 | 0.02 | 0.01 | 0.05 | 0.05 | 0.00 | 0.04 | 0.01 | 0.04 | 0.03 | 0.05 | 0.06 | 0.06 | 0.00 | 0.01 | 0.00 | 0.00 | 0.06 | 0.04 | 0.24 | 0.08 | 0.04 | 0.00 | 0.07 | 0.03 | 0.32 | 0.03 | 0.18 | 0.05 | 0.25 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.03 | 0.03 | 0.00 | 0.00 | 0.12 | 0.03 |
| SLC16A8 | ENSG00000100156 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.09 | 0.05 | 0.00 | 0.05 | 0.00 | 0.03 | 0.08 | 0.03 | 0.10 | 0.02 | 0.01 | 0.01 | 0.05 | 0.02 | 0.02 | 0.01 | 0.01 | 0.02 | 0.02 | 0.01 | 0.02 | 0.02 | 0.06 | 0.00 | 0.00 | 0.01 | 0.04 | 0.01 | 0.00 | 0.04 | 0.00 | 0.00 | 0.03 | 0.03 | 0.12 | 0.11 | 0.03 | 0.02 | 0.10 | 0.02 | 0.33 | 0.10 | 0.06 | 0.03 | 0.01 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.01 | 0.04 | 0.02 | 0.00 | 0.21 | 0.01 |
| CYP2D6 | ENSG00000100197 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.03 | 0.01 | 0.08 | 0.00 | 0.03 | 0.00 | 0.04 | 0.04 | 0.04 | 0.06 | 0.02 | 0.02 | 0.01 | 0.04 | 0.00 | 0.02 | 0.03 | 0.00 | 0.03 | 0.01 | 0.06 | 0.03 | 0.04 | 0.03 | 0.03 | 0.04 | 0.01 | 0.02 | 0.00 | 0.00 | 0.06 | 0.00 | 0.00 | 0.03 | 0.04 | 0.01 | 0.31 | 0.04 | 0.05 | 0.02 | 0.07 | 0.06 | 0.23 | 0.05 | 0.07 | 0.00 | 0.03 | 0.00 | 0.00 | 0.02 | 0.07 | 0.00 | 0.03 | 0.01 | 0.07 | 0.00 | 0.00 | 0.27 | 0.01 |
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