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 |
| ADM | ENSG00000148926 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.01 | 0.01 | 0.09 | 0.00 | 0.00 | 0.02 | 0.04 | 0.04 | 0.06 | 0.03 | 0.14 | 0.02 | 0.05 | 0.08 | 0.07 | 0.03 | 0.03 | 0.01 | 0.01 | 0.01 | 0.01 | 0.01 | 0.03 | 0.05 | 0.02 | 0.00 | 0.03 | 0.01 | 0.04 | 0.02 | 0.06 | 0.00 | 0.00 | 0.03 | 0.09 | 0.02 | 0.39 | 0.01 | 0.06 | 0.03 | 0.06 | 0.03 | 0.05 | 0.04 | 0.10 | 0.02 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.01 | 0.08 | 0.00 | 0.04 | 0.00 | 0.00 | 0.02 | 0.04 |
| SLC5A12 | ENSG00000148942 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.05 | 0.06 | 0.00 | 0.00 | 0.00 | 0.04 | 0.05 | 0.02 | 0.06 | 0.04 | 0.02 | 0.03 | 0.14 | 0.02 | 0.05 | 0.02 | 0.02 | 0.00 | 0.00 | 0.02 | 0.01 | 0.02 | 0.03 | 0.00 | 0.00 | 0.01 | 0.02 | 0.01 | 0.02 | 0.03 | 0.00 | 0.00 | 0.07 | 0.04 | 0.11 | 0.12 | 0.00 | 0.04 | 0.04 | 0.03 | 0.01 | 0.11 | 0.06 | 0.08 | 0.01 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.02 |
| SAA4 | ENSG00000148965 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.03 | 0.01 | 0.01 | 0.01 | 0.07 | 0.00 | 0.00 | 0.02 | 0.03 | 0.02 | 0.04 | 0.06 | 0.07 | 0.01 | 0.05 | 0.04 | 0.03 | 0.02 | 0.02 | 0.02 | 0.00 | 0.01 | 0.01 | 0.00 | 0.02 | 0.04 | 0.02 | 0.03 | 0.01 | 0.00 | 0.02 | 0.06 | 0.04 | 0.00 | 0.00 | 0.06 | 0.05 | 0.05 | 0.24 | 0.01 | 0.04 | 0.03 | 0.04 | 0.01 | 0.04 | 0.09 | 0.07 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.03 | 0.01 |
| SCGB1A1 | ENSG00000149021 | 0.00 | 0.00 | 0.00 | 0.01 | 0.09 | 0.00 | 0.01 | 0.01 | 0.14 | 0.01 | 0.00 | 0.00 | 0.12 | 0.00 | 0.05 | 0.02 | 0.06 | 0.02 | 0.14 | 0.02 | 0.13 | 0.02 | 0.03 | 0.02 | 0.01 | 0.02 | 0.02 | 0.03 | 0.00 | 0.03 | 0.08 | 0.02 | 0.08 | 0.07 | 0.08 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.09 | 0.07 | 0.18 | 0.04 | 0.06 | 0.01 | 0.11 | 0.01 | 0.33 | 0.12 | 0.07 | 0.03 | 0.00 | 0.06 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.04 | 0.05 |
| OR5F1 | ENSG00000149133 | 0.01 | 0.00 | 0.00 | 0.01 | 0.08 | 0.00 | 0.01 | 0.03 | 0.13 | 0.04 | 0.00 | 0.01 | 0.04 | 0.03 | 0.04 | 0.03 | 0.08 | 0.03 | 0.11 | 0.01 | 0.16 | 0.05 | 0.01 | 0.04 | 0.02 | 0.01 | 0.01 | 0.02 | 0.00 | 0.01 | 0.02 | 0.02 | 0.05 | 0.07 | 0.07 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.09 | 0.07 | 0.12 | 0.06 | 0.04 | 0.02 | 0.04 | 0.03 | 0.34 | 0.03 | 0.10 | 0.05 | 0.01 | 0.03 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.02 | 0.01 | 0.02 | 0.00 | 0.02 | 0.05 | 0.04 |
| SLC43A1 | ENSG00000149150 | 0.00 | 0.00 | 0.00 | 0.01 | 0.09 | 0.00 | 0.00 | 0.01 | 0.14 | 0.02 | 0.00 | 0.00 | 0.06 | 0.02 | 0.05 | 0.03 | 0.08 | 0.02 | 0.11 | 0.01 | 0.14 | 0.04 | 0.01 | 0.04 | 0.01 | 0.01 | 0.01 | 0.03 | 0.00 | 0.02 | 0.04 | 0.02 | 0.00 | 0.12 | 0.04 | 0.00 | 0.02 | 0.03 | 0.00 | 0.00 | 0.11 | 0.06 | 0.10 | 0.05 | 0.07 | 0.02 | 0.06 | 0.02 | 0.36 | 0.09 | 0.09 | 0.04 | 0.01 | 0.03 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.02 | 0.01 | 0.03 | 0.00 | 0.00 | 0.04 | 0.02 |
| ENDOD1 | ENSG00000149218 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.03 | 0.04 | 0.03 | 0.09 | 0.05 | 0.00 | 0.00 | 0.06 | 0.06 | 0.09 | 0.04 | 0.06 | 0.09 | 0.07 | 0.10 | 0.10 | 0.07 | 0.05 | 0.04 | 0.02 | 0.01 | 0.02 | 0.01 | 0.01 | 0.01 | 0.02 | 0.05 | 0.00 | 0.10 | 0.00 | 0.02 | 0.00 | 0.04 | 0.00 | 0.00 | 0.09 | 0.13 | 0.31 | 0.10 | 0.19 | 0.08 | 0.06 | 0.03 | 0.18 | 0.16 | 0.05 | 0.14 | 0.01 | 0.07 | 0.00 | 0.00 | 0.03 | 0.01 | 0.02 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.11 | 0.10 |
| NCAM1 | ENSG00000149294 | 0.01 | 0.02 | 0.00 | 0.07 | 0.02 | 0.05 | 0.01 | 0.10 | 0.03 | 0.11 | 0.00 | 0.00 | 0.02 | 0.17 | 0.04 | 0.09 | 0.05 | 0.10 | 0.03 | 0.16 | 0.06 | 0.13 | 0.04 | 0.09 | 0.01 | 0.03 | 0.00 | 0.04 | 0.01 | 0.01 | 0.00 | 0.08 | 0.01 | 0.20 | 0.00 | 0.09 | 0.01 | 0.09 | 0.00 | 0.00 | 0.02 | 0.24 | 0.15 | 0.17 | 0.04 | 0.30 | 0.02 | 0.07 | 0.09 | 0.20 | 0.02 | 0.24 | 0.00 | 0.17 | 0.02 | 0.00 | 0.10 | 0.01 | 0.02 | 0.01 | 0.01 | 0.01 | 0.00 | 0.04 | 0.01 | 0.27 |
| DRD2 | ENSG00000149295 | 0.01 | 0.01 | 0.00 | 0.07 | 0.02 | 0.02 | 0.00 | 0.10 | 0.02 | 0.11 | 0.00 | 0.00 | 0.02 | 0.17 | 0.03 | 0.09 | 0.04 | 0.09 | 0.03 | 0.16 | 0.04 | 0.13 | 0.04 | 0.09 | 0.01 | 0.02 | 0.00 | 0.04 | 0.01 | 0.01 | 0.01 | 0.08 | 0.01 | 0.20 | 0.00 | 0.07 | 0.00 | 0.06 | 0.00 | 0.00 | 0.02 | 0.24 | 0.15 | 0.16 | 0.04 | 0.30 | 0.02 | 0.07 | 0.09 | 0.20 | 0.02 | 0.24 | 0.00 | 0.17 | 0.02 | 0.00 | 0.10 | 0.01 | 0.02 | 0.01 | 0.01 | 0.01 | 0.00 | 0.04 | 0.03 | 0.27 |
| HTR3B | ENSG00000149305 | 0.00 | 0.01 | 0.00 | 0.07 | 0.02 | 0.02 | 0.00 | 0.12 | 0.02 | 0.11 | 0.00 | 0.00 | 0.02 | 0.19 | 0.03 | 0.10 | 0.04 | 0.09 | 0.03 | 0.16 | 0.03 | 0.13 | 0.04 | 0.09 | 0.01 | 0.02 | 0.00 | 0.04 | 0.01 | 0.01 | 0.00 | 0.08 | 0.01 | 0.20 | 0.00 | 0.07 | 0.01 | 0.06 | 0.00 | 0.00 | 0.01 | 0.24 | 0.14 | 0.16 | 0.04 | 0.30 | 0.02 | 0.07 | 0.09 | 0.20 | 0.03 | 0.22 | 0.00 | 0.19 | 0.02 | 0.00 | 0.10 | 0.01 | 0.02 | 0.01 | 0.01 | 0.01 | 0.00 | 0.04 | 0.02 | 0.28 |
| HYOU1 | ENSG00000149428 | 0.01 | 0.01 | 0.01 | 0.05 | 0.02 | 0.02 | 0.02 | 0.08 | 0.04 | 0.11 | 0.00 | 0.00 | 0.11 | 0.04 | 0.05 | 0.07 | 0.05 | 0.09 | 0.04 | 0.16 | 0.05 | 0.12 | 0.06 | 0.07 | 0.00 | 0.01 | 0.03 | 0.03 | 0.01 | 0.02 | 0.02 | 0.09 | 0.00 | 0.17 | 0.03 | 0.05 | 0.00 | 0.06 | 0.00 | 0.00 | 0.02 | 0.21 | 0.15 | 0.14 | 0.04 | 0.30 | 0.06 | 0.05 | 0.16 | 0.17 | 0.04 | 0.22 | 0.00 | 0.15 | 0.03 | 0.01 | 0.14 | 0.01 | 0.06 | 0.01 | 0.03 | 0.01 | 0.00 | 0.07 | 0.01 | 0.25 |
| GGTLC1 | ENSG00000149435 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.02 | 0.04 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.08 | 0.02 | 0.05 | 0.03 | 0.05 | 0.02 | 0.10 | 0.02 | 0.05 | 0.01 | 0.05 | 0.01 | 0.03 | 0.02 | 0.04 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.04 | 0.03 | 0.09 | 0.03 | 0.04 | 0.02 | 0.03 | 0.01 | 0.05 | 0.00 | 0.07 | 0.01 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.00 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.02 |
| ZP1 | ENSG00000149506 | 0.01 | 0.00 | 0.00 | 0.01 | 0.09 | 0.00 | 0.01 | 0.01 | 0.12 | 0.01 | 0.00 | 0.00 | 0.07 | 0.02 | 0.06 | 0.03 | 0.06 | 0.02 | 0.12 | 0.02 | 0.13 | 0.03 | 0.04 | 0.03 | 0.01 | 0.01 | 0.05 | 0.02 | 0.00 | 0.02 | 0.03 | 0.02 | 0.04 | 0.09 | 0.06 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.13 | 0.07 | 0.11 | 0.05 | 0.05 | 0.03 | 0.04 | 0.02 | 0.14 | 0.14 | 0.06 | 0.02 | 0.00 | 0.05 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.02 | 0.00 | 0.03 | 0.00 | 0.00 | 0.05 | 0.04 |
| ESAM | ENSG00000149564 | 0.00 | 0.01 | 0.00 | 0.05 | 0.02 | 0.02 | 0.02 | 0.06 | 0.03 | 0.09 | 0.00 | 0.00 | 0.11 | 0.06 | 0.05 | 0.09 | 0.04 | 0.11 | 0.04 | 0.14 | 0.04 | 0.16 | 0.05 | 0.08 | 0.01 | 0.01 | 0.01 | 0.03 | 0.01 | 0.02 | 0.00 | 0.09 | 0.00 | 0.19 | 0.00 | 0.06 | 0.00 | 0.05 | 0.00 | 0.00 | 0.02 | 0.22 | 0.19 | 0.17 | 0.04 | 0.31 | 0.04 | 0.07 | 0.05 | 0.17 | 0.06 | 0.23 | 0.00 | 0.24 | 0.03 | 0.00 | 0.13 | 0.02 | 0.07 | 0.01 | 0.01 | 0.02 | 0.00 | 0.07 | 0.01 | 0.26 |
| SCN2B | ENSG00000149575 | 0.01 | 0.01 | 0.00 | 0.06 | 0.02 | 0.02 | 0.02 | 0.08 | 0.04 | 0.11 | 0.00 | 0.00 | 0.07 | 0.06 | 0.05 | 0.07 | 0.05 | 0.09 | 0.05 | 0.16 | 0.04 | 0.11 | 0.07 | 0.07 | 0.01 | 0.01 | 0.03 | 0.03 | 0.01 | 0.02 | 0.02 | 0.09 | 0.00 | 0.17 | 0.03 | 0.05 | 0.00 | 0.06 | 0.00 | 0.00 | 0.03 | 0.23 | 0.14 | 0.15 | 0.05 | 0.30 | 0.05 | 0.05 | 0.15 | 0.16 | 0.05 | 0.21 | 0.00 | 0.15 | 0.02 | 0.00 | 0.14 | 0.01 | 0.07 | 0.01 | 0.01 | 0.01 | 0.00 | 0.07 | 0.01 | 0.27 |
| TMEM25 | ENSG00000149582 | 0.01 | 0.01 | 0.00 | 0.06 | 0.02 | 0.02 | 0.02 | 0.08 | 0.04 | 0.11 | 0.00 | 0.02 | 0.09 | 0.04 | 0.06 | 0.08 | 0.04 | 0.09 | 0.05 | 0.16 | 0.04 | 0.12 | 0.08 | 0.07 | 0.01 | 0.01 | 0.03 | 0.03 | 0.01 | 0.02 | 0.01 | 0.09 | 0.00 | 0.17 | 0.03 | 0.05 | 0.00 | 0.06 | 0.00 | 0.00 | 0.03 | 0.21 | 0.18 | 0.14 | 0.04 | 0.30 | 0.06 | 0.04 | 0.25 | 0.15 | 0.03 | 0.23 | 0.00 | 0.15 | 0.03 | 0.03 | 0.14 | 0.01 | 0.07 | 0.01 | 0.03 | 0.01 | 0.00 | 0.07 | 0.00 | 0.26 |
| SOGA1 | ENSG00000149639 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.01 | 0.03 | 0.06 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.07 | 0.01 | 0.10 | 0.01 | 0.07 | 0.01 | 0.10 | 0.01 | 0.10 | 0.01 | 0.08 | 0.00 | 0.18 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.00 | 0.04 | 0.06 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.10 | 0.02 | 0.14 | 0.06 | 0.06 | 0.01 | 0.07 | 0.01 | 0.14 | 0.00 | 0.08 | 0.04 | 0.00 | 0.01 | 0.00 | 0.02 | 0.01 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.05 | 0.00 |
| SPINT4 | ENSG00000149651 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.01 | 0.11 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.05 | 0.07 | 0.01 | 0.01 | 0.01 | 0.05 | 0.00 | 0.18 | 0.00 | 0.18 | 0.00 | 0.13 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.00 | 0.01 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.14 | 0.02 | 0.22 | 0.04 | 0.02 | 0.04 | 0.08 | 0.01 | 0.29 | 0.00 | 0.10 | 0.03 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.07 | 0.01 |
| GPHA2 | ENSG00000149735 | 0.01 | 0.00 | 0.00 | 0.01 | 0.07 | 0.00 | 0.03 | 0.01 | 0.11 | 0.01 | 0.00 | 0.00 | 0.08 | 0.00 | 0.07 | 0.03 | 0.07 | 0.02 | 0.19 | 0.02 | 0.15 | 0.04 | 0.04 | 0.03 | 0.01 | 0.02 | 0.04 | 0.04 | 0.00 | 0.03 | 0.02 | 0.04 | 0.00 | 0.11 | 0.07 | 0.07 | 0.01 | 0.01 | 0.00 | 0.00 | 0.09 | 0.09 | 0.19 | 0.04 | 0.10 | 0.01 | 0.09 | 0.03 | 0.22 | 0.06 | 0.09 | 0.03 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.05 | 0.06 |
| TAOK2 | ENSG00000149930 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.17 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.09 | 0.01 | 0.09 | 0.01 | 0.03 | 0.01 | 0.12 | 0.00 | 0.05 | 0.00 | 0.05 | 0.00 | 0.05 | 0.00 | 0.00 | 0.00 | 0.04 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.08 | 0.01 | 0.12 | 0.03 | 0.02 | 0.02 | 0.10 | 0.01 | 0.34 | 0.05 | 0.04 | 0.04 | 0.00 | 0.02 | 0.00 | 0.01 | 0.02 | 0.00 | 0.00 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.02 |
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