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 |
| SPAM1 | ENSG00000106304 | 0.01 | 0.01 | 0.05 | 0.01 | 0.01 | 0.00 | 0.02 | 0.04 | 0.03 | 0.04 | 0.00 | 0.01 | 0.04 | 0.08 | 0.06 | 0.03 | 0.09 | 0.06 | 0.03 | 0.11 | 0.03 | 0.17 | 0.03 | 0.07 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 | 0.04 | 0.05 | 0.04 | 0.00 | 0.02 | 0.01 | 0.06 | 0.00 | 0.04 | 0.00 | 0.00 | 0.06 | 0.04 | 0.27 | 0.06 | 0.04 | 0.07 | 0.01 | 0.05 | 0.05 | 0.12 | 0.11 | 0.03 | 0.03 | 0.02 | 0.00 | 0.05 | 0.09 | 0.07 | 0.10 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.17 | 0.02 |
| PCOLCE | ENSG00000106333 | 0.02 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.06 | 0.01 | 0.08 | 0.01 | 0.00 | 0.00 | 0.03 | 0.00 | 0.12 | 0.01 | 0.22 | 0.02 | 0.22 | 0.01 | 0.50 | 0.02 | 0.27 | 0.01 | 0.02 | 0.00 | 0.01 | 0.00 | 0.08 | 0.01 | 0.07 | 0.02 | 0.11 | 0.01 | 0.10 | 0.03 | 0.00 | 0.02 | 0.00 | 0.00 | 0.09 | 0.03 | 0.22 | 0.05 | 0.08 | 0.01 | 0.07 | 0.02 | 0.19 | 0.03 | 0.06 | 0.04 | 0.07 | 0.01 | 0.00 | 0.00 | 0.13 | 0.00 | 0.06 | 0.00 | 0.03 | 0.01 | 0.00 | 0.00 | 0.05 | 0.03 |
| IMPDH1 | ENSG00000106348 | 0.01 | 0.01 | 0.08 | 0.00 | 0.01 | 0.00 | 0.02 | 0.05 | 0.05 | 0.04 | 0.00 | 0.01 | 0.04 | 0.07 | 0.07 | 0.02 | 0.07 | 0.07 | 0.02 | 0.13 | 0.03 | 0.19 | 0.04 | 0.06 | 0.03 | 0.01 | 0.06 | 0.02 | 0.01 | 0.04 | 0.05 | 0.05 | 0.00 | 0.02 | 0.01 | 0.06 | 0.00 | 0.02 | 0.00 | 0.00 | 0.09 | 0.04 | 0.36 | 0.04 | 0.03 | 0.07 | 0.07 | 0.05 | 0.11 | 0.14 | 0.10 | 0.02 | 0.03 | 0.03 | 0.00 | 0.06 | 0.02 | 0.11 | 0.12 | 0.00 | 0.06 | 0.00 | 0.00 | 0.00 | 0.18 | 0.02 |
| SERPINE1 | ENSG00000106366 | 0.02 | 0.00 | 0.05 | 0.00 | 0.02 | 0.00 | 0.04 | 0.02 | 0.07 | 0.02 | 0.00 | 0.00 | 0.03 | 0.00 | 0.09 | 0.02 | 0.22 | 0.02 | 0.21 | 0.01 | 0.46 | 0.02 | 0.19 | 0.02 | 0.02 | 0.01 | 0.01 | 0.00 | 0.06 | 0.02 | 0.05 | 0.02 | 0.11 | 0.01 | 0.08 | 0.03 | 0.01 | 0.02 | 0.00 | 0.00 | 0.06 | 0.04 | 0.22 | 0.05 | 0.05 | 0.02 | 0.05 | 0.02 | 0.15 | 0.03 | 0.07 | 0.04 | 0.07 | 0.01 | 0.00 | 0.00 | 0.13 | 0.00 | 0.07 | 0.00 | 0.03 | 0.01 | 0.00 | 0.00 | 0.06 | 0.03 |
| MEST | ENSG00000106484 | 0.01 | 0.01 | 0.13 | 0.00 | 0.01 | 0.00 | 0.02 | 0.04 | 0.04 | 0.04 | 0.00 | 0.01 | 0.04 | 0.05 | 0.08 | 0.02 | 0.06 | 0.06 | 0.02 | 0.13 | 0.05 | 0.18 | 0.03 | 0.07 | 0.02 | 0.00 | 0.03 | 0.02 | 0.01 | 0.04 | 0.05 | 0.04 | 0.00 | 0.02 | 0.01 | 0.06 | 0.00 | 0.01 | 0.00 | 0.00 | 0.09 | 0.03 | 0.40 | 0.03 | 0.02 | 0.07 | 0.06 | 0.05 | 0.15 | 0.14 | 0.15 | 0.03 | 0.02 | 0.03 | 0.00 | 0.05 | 0.02 | 0.11 | 0.13 | 0.00 | 0.07 | 0.00 | 0.00 | 0.00 | 0.20 | 0.01 |
| AGR2 | ENSG00000106541 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.02 | 0.26 | 0.01 | 0.00 | 0.00 | 0.08 | 0.00 | 0.12 | 0.01 | 0.11 | 0.01 | 0.08 | 0.01 | 0.22 | 0.02 | 0.12 | 0.01 | 0.05 | 0.00 | 0.03 | 0.00 | 0.01 | 0.00 | 0.06 | 0.00 | 0.00 | 0.01 | 0.11 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.08 | 0.04 | 0.12 | 0.29 | 0.04 | 0.01 | 0.08 | 0.03 | 0.12 | 0.03 | 0.17 | 0.03 | 0.09 | 0.00 | 0.00 | 0.02 | 0.03 | 0.06 | 0.00 | 0.01 | 0.05 | 0.01 | 0.00 | 0.00 | 0.12 | 0.02 |
| PSMA2 | ENSG00000106588 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.06 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.07 | 0.02 | 0.03 | 0.01 | 0.10 | 0.03 | 0.02 | 0.01 | 0.03 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.00 | 0.01 | 0.07 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.02 | 0.09 | 0.08 | 0.03 | 0.00 | 0.03 | 0.02 | 0.02 | 0.00 | 0.07 | 0.04 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.02 | 0.01 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.04 | 0.03 |
| EIF4H | ENSG00000106682 | 0.02 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.04 | 0.02 | 0.00 | 0.00 | 0.02 | 0.00 | 0.02 | 0.02 | 0.07 | 0.03 | 0.04 | 0.03 | 0.22 | 0.03 | 0.07 | 0.02 | 0.01 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.06 | 0.01 | 0.00 | 0.01 | 0.15 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.08 | 0.02 | 0.17 | 0.06 | 0.05 | 0.02 | 0.05 | 0.02 | 0.03 | 0.00 | 0.08 | 0.05 | 0.12 | 0.00 | 0.00 | 0.00 | 0.15 | 0.00 | 0.01 | 0.01 | 0.07 | 0.00 | 0.00 | 0.00 | 0.06 | 0.02 |
| CNTNAP3 | ENSG00000106714 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.03 | 0.01 | 0.08 | 0.08 | 0.00 | 0.03 | 0.01 | 0.11 | 0.04 | 0.13 | 0.19 | 0.13 | 0.09 | 0.11 | 0.17 | 0.08 | 0.07 | 0.09 | 0.01 | 0.01 | 0.03 | 0.03 | 0.06 | 0.02 | 0.03 | 0.06 | 0.19 | 0.25 | 0.07 | 0.04 | 0.00 | 0.02 | 0.00 | 0.00 | 0.05 | 0.08 | 0.11 | 0.18 | 0.02 | 0.03 | 0.03 | 0.05 | 0.01 | 0.22 | 0.14 | 0.08 | 0.02 | 0.02 | 0.00 | 0.02 | 0.03 | 0.00 | 0.00 | 0.02 | 0.01 | 0.09 | 0.00 | 0.03 | 0.06 | 0.09 |
| SPIN1 | ENSG00000106723 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.02 | 0.06 | 0.03 | 0.00 | 0.02 | 0.01 | 0.05 | 0.02 | 0.03 | 0.04 | 0.03 | 0.02 | 0.00 | 0.06 | 0.01 | 0.03 | 0.04 | 0.02 | 0.01 | 0.02 | 0.01 | 0.00 | 0.00 | 0.01 | 0.02 | 0.00 | 0.15 | 0.02 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.03 | 0.03 | 0.05 | 0.14 | 0.00 | 0.02 | 0.05 | 0.03 | 0.03 | 0.15 | 0.15 | 0.01 | 0.04 | 0.02 | 0.00 | 0.02 | 0.05 | 0.02 | 0.00 | 0.00 | 0.01 | 0.02 | 0.00 | 0.00 | 0.00 | 0.02 |
| OGN | ENSG00000106809 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.01 | 0.06 | 0.04 | 0.00 | 0.01 | 0.01 | 0.05 | 0.01 | 0.05 | 0.04 | 0.03 | 0.04 | 0.01 | 0.08 | 0.01 | 0.03 | 0.04 | 0.01 | 0.01 | 0.04 | 0.02 | 0.00 | 0.01 | 0.01 | 0.03 | 0.00 | 0.08 | 0.04 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.03 | 0.04 | 0.04 | 0.16 | 0.02 | 0.03 | 0.03 | 0.05 | 0.03 | 0.16 | 0.10 | 0.01 | 0.05 | 0.02 | 0.00 | 0.02 | 0.04 | 0.05 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.02 |
| ASPN | ENSG00000106819 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.01 | 0.07 | 0.04 | 0.00 | 0.01 | 0.01 | 0.05 | 0.01 | 0.05 | 0.04 | 0.03 | 0.04 | 0.01 | 0.09 | 0.01 | 0.03 | 0.04 | 0.01 | 0.01 | 0.04 | 0.02 | 0.00 | 0.01 | 0.01 | 0.03 | 0.00 | 0.08 | 0.04 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.04 | 0.04 | 0.04 | 0.16 | 0.02 | 0.03 | 0.02 | 0.05 | 0.03 | 0.16 | 0.10 | 0.01 | 0.05 | 0.02 | 0.00 | 0.02 | 0.04 | 0.05 | 0.00 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.01 | 0.02 |
| ECM2 | ENSG00000106823 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.01 | 0.07 | 0.04 | 0.00 | 0.01 | 0.01 | 0.05 | 0.01 | 0.05 | 0.04 | 0.03 | 0.04 | 0.01 | 0.09 | 0.01 | 0.03 | 0.04 | 0.01 | 0.01 | 0.04 | 0.02 | 0.00 | 0.01 | 0.01 | 0.03 | 0.00 | 0.08 | 0.04 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.04 | 0.04 | 0.04 | 0.16 | 0.02 | 0.03 | 0.02 | 0.05 | 0.03 | 0.16 | 0.10 | 0.01 | 0.05 | 0.02 | 0.00 | 0.02 | 0.04 | 0.05 | 0.00 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.01 | 0.02 |
| RLN2 | ENSG00000107014 | 0.01 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.05 | 0.18 | 0.12 | 0.01 | 0.01 | 0.04 | 0.07 | 0.06 | 0.11 | 0.15 | 0.10 | 0.25 | 0.05 | 0.15 | 0.13 | 0.17 | 0.10 | 0.01 | 0.03 | 0.04 | 0.04 | 0.01 | 0.08 | 0.06 | 0.03 | 0.03 | 0.01 | 0.12 | 0.03 | 0.00 | 0.03 | 0.00 | 0.00 | 0.10 | 0.06 | 0.17 | 0.19 | 0.26 | 0.03 | 0.07 | 0.02 | 0.02 | 0.12 | 0.21 | 0.11 | 0.01 | 0.09 | 0.00 | 0.00 | 0.07 | 0.05 | 0.00 | 0.09 | 0.01 | 0.18 | 0.00 | 0.00 | 0.09 | 0.11 |
| RLN1 | ENSG00000107018 | 0.01 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.05 | 0.18 | 0.12 | 0.01 | 0.01 | 0.04 | 0.07 | 0.06 | 0.11 | 0.16 | 0.10 | 0.25 | 0.05 | 0.15 | 0.13 | 0.17 | 0.10 | 0.01 | 0.03 | 0.04 | 0.04 | 0.01 | 0.08 | 0.06 | 0.03 | 0.03 | 0.01 | 0.12 | 0.03 | 0.00 | 0.03 | 0.00 | 0.00 | 0.10 | 0.06 | 0.17 | 0.19 | 0.29 | 0.03 | 0.07 | 0.02 | 0.02 | 0.12 | 0.24 | 0.11 | 0.01 | 0.09 | 0.00 | 0.00 | 0.07 | 0.05 | 0.00 | 0.09 | 0.01 | 0.18 | 0.00 | 0.00 | 0.09 | 0.11 |
| KDM4C | ENSG00000107077 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.06 | 0.17 | 0.13 | 0.01 | 0.01 | 0.04 | 0.06 | 0.06 | 0.14 | 0.13 | 0.11 | 0.24 | 0.06 | 0.13 | 0.13 | 0.09 | 0.11 | 0.01 | 0.03 | 0.04 | 0.04 | 0.04 | 0.10 | 0.05 | 0.03 | 0.03 | 0.01 | 0.02 | 0.03 | 0.01 | 0.03 | 0.00 | 0.00 | 0.10 | 0.06 | 0.17 | 0.19 | 0.20 | 0.04 | 0.07 | 0.03 | 0.02 | 0.17 | 0.21 | 0.13 | 0.01 | 0.09 | 0.00 | 0.00 | 0.04 | 0.02 | 0.01 | 0.10 | 0.02 | 0.20 | 0.00 | 0.00 | 0.04 | 0.12 |
| TESK1 | ENSG00000107140 | 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 | 0.02 | 0.38 | 0.04 | 0.30 | 0.03 | 0.35 | 0.02 | 0.16 | 0.02 | 0.02 | 0.01 | 0.00 | 0.00 | 0.20 | 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 | 0.05 | 0.01 | 0.00 | 0.13 | 0.14 | 0.04 | 0.03 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.05 | 0.06 | 0.00 | 0.03 | 0.08 | 0.05 |
| CA9 | ENSG00000107159 | 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 | 0.06 | 0.02 | 0.39 | 0.04 | 0.30 | 0.03 | 0.33 | 0.02 | 0.18 | 0.02 | 0.02 | 0.01 | 0.02 | 0.00 | 0.21 | 0.00 | 0.04 | 0.02 | 0.19 | 0.01 | 0.20 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.08 | 0.02 | 0.13 | 0.06 | 0.03 | 0.01 | 0.07 | 0.01 | 0.02 | 0.13 | 0.14 | 0.04 | 0.03 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.05 | 0.06 | 0.00 | 0.03 | 0.08 | 0.05 |
| PTGDS | ENSG00000107317 | 0.00 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.03 | 0.01 | 0.07 | 0.02 | 0.00 | 0.01 | 0.00 | 0.02 | 0.07 | 0.03 | 0.08 | 0.03 | 0.09 | 0.05 | 0.20 | 0.01 | 0.17 | 0.02 | 0.03 | 0.01 | 0.10 | 0.05 | 0.03 | 0.00 | 0.07 | 0.04 | 0.06 | 0.01 | 0.14 | 0.02 | 0.02 | 0.01 | 0.00 | 0.00 | 0.06 | 0.05 | 0.21 | 0.22 | 0.07 | 0.03 | 0.12 | 0.03 | 0.22 | 0.14 | 0.07 | 0.16 | 0.03 | 0.03 | 0.01 | 0.00 | 0.05 | 0.00 | 0.02 | 0.01 | 0.04 | 0.01 | 0.00 | 0.00 | 0.04 | 0.03 |
| CXCL12 | ENSG00000107562 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.04 | 0.08 | 0.04 | 0.07 | 0.00 | 0.01 | 0.04 | 0.05 | 0.02 | 0.08 | 0.03 | 0.06 | 0.02 | 0.11 | 0.06 | 0.03 | 0.01 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.01 | 0.03 | 0.01 | 0.15 | 0.01 | 0.07 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.06 | 0.03 | 0.08 | 0.11 | 0.01 | 0.02 | 0.02 | 0.03 | 0.05 | 0.03 | 0.08 | 0.08 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.03 |
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