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 |
| WNT9B | ENSG00000158955 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.07 | 0.09 | 0.02 | 0.01 | 0.00 | 0.06 | 0.00 | 0.07 | 0.01 | 0.07 | 0.02 | 0.02 | 0.01 | 0.09 | 0.03 | 0.06 | 0.01 | 0.02 | 0.01 | 0.04 | 0.02 | 0.03 | 0.02 | 0.02 | 0.02 | 0.02 | 0.01 | 0.04 | 0.08 | 0.01 | 0.06 | 0.00 | 0.00 | 0.11 | 0.08 | 0.05 | 0.08 | 0.02 | 0.02 | 0.04 | 0.06 | 0.11 | 0.19 | 0.07 | 0.04 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.01 | 0.01 | 0.03 | 0.03 | 0.04 | 0.05 |
| OTOA | ENSG00000155719 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.12 | 0.04 | 0.00 | 0.00 | 0.00 | 0.04 | 0.03 | 0.02 | 0.03 | 0.02 | 0.02 | 0.02 | 0.03 | 0.02 | 0.02 | 0.01 | 0.03 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.12 | 0.06 | 0.02 | 0.01 | 0.06 | 0.01 | 0.06 | 0.00 | 0.03 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.04 | 0.00 | 0.00 | 0.02 | 0.00 | 0.07 | 0.00 | 0.00 | 0.00 | 0.03 |
| UTS2B | ENSG00000188958 | 0.05 | 0.00 | 0.03 | 0.01 | 0.00 | 0.01 | 0.03 | 0.05 | 0.15 | 0.01 | 0.00 | 0.00 | 0.00 | 0.07 | 0.13 | 0.05 | 1.41 | 0.01 | 0.58 | 0.00 | 0.74 | 0.02 | 0.22 | 0.02 | 0.05 | 0.01 | 0.06 | 0.02 | 0.03 | 0.00 | 0.11 | 0.04 | 0.12 | 0.03 | 0.10 | 0.00 | 0.00 | 0.10 | 0.00 | 0.00 | 0.20 | 0.02 | 0.96 | 0.08 | 0.63 | 0.00 | 0.34 | 0.01 | 0.79 | 0.11 | 0.15 | 0.10 | 0.23 | 0.01 | 0.01 | 0.00 | 0.07 | 0.04 | 0.02 | 0.05 | 0.07 | 0.09 | 0.00 | 0.00 | 0.03 | 0.04 |
| SLC12A1 | ENSG00000074803 | 0.00 | 0.00 | 0.00 | 0.01 | 0.14 | 0.00 | 0.01 | 0.04 | 0.03 | 0.05 | 0.00 | 0.00 | 0.02 | 0.18 | 0.01 | 0.06 | 0.03 | 0.06 | 0.02 | 0.03 | 0.02 | 0.04 | 0.01 | 0.06 | 0.01 | 0.04 | 0.00 | 0.05 | 0.00 | 0.02 | 0.00 | 0.02 | 0.00 | 0.01 | 0.02 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.08 | 0.06 | 0.24 | 0.00 | 0.10 | 0.00 | 0.07 | 0.08 | 0.26 | 0.07 | 0.07 | 0.01 | 0.04 | 0.00 | 0.00 | 0.02 | 0.05 | 0.00 | 0.03 | 0.00 | 0.11 | 0.00 | 0.00 | 0.03 | 0.13 |
| ESR2 | ENSG00000140009 | 0.01 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.03 | 0.03 | 0.05 | 0.00 | 0.01 | 0.00 | 0.03 | 0.05 | 0.04 | 0.04 | 0.05 | 0.08 | 0.02 | 0.05 | 0.04 | 0.05 | 0.04 | 0.01 | 0.03 | 0.01 | 0.03 | 0.01 | 0.00 | 0.02 | 0.09 | 0.00 | 0.29 | 0.15 | 0.03 | 0.01 | 0.03 | 0.00 | 0.00 | 0.04 | 0.08 | 0.05 | 0.27 | 0.02 | 0.02 | 0.02 | 0.03 | 0.07 | 0.04 | 0.04 | 0.10 | 0.02 | 0.01 | 0.00 | 0.00 | 0.04 | 0.00 | 0.00 | 0.12 | 0.00 | 0.07 | 0.03 | 0.00 | 0.01 | 0.04 |
| SERPINA12 | ENSG00000165953 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.04 | 0.02 | 0.04 | 0.04 | 0.06 | 0.00 | 0.00 | 0.00 | 0.05 | 0.03 | 0.06 | 0.12 | 0.02 | 0.05 | 0.04 | 0.07 | 0.06 | 0.03 | 0.05 | 0.00 | 0.03 | 0.01 | 0.02 | 0.01 | 0.02 | 0.02 | 0.09 | 0.00 | 0.31 | 0.05 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.04 | 0.09 | 0.21 | 0.17 | 0.08 | 0.09 | 0.04 | 0.03 | 0.06 | 0.02 | 0.09 | 0.09 | 0.03 | 0.01 | 0.00 | 0.00 | 0.03 | 0.04 | 0.00 | 0.10 | 0.02 | 0.06 | 0.03 | 0.01 | 0.01 | 0.06 |
| ZP2 | ENSG00000103310 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.12 | 0.03 | 0.00 | 0.00 | 0.01 | 0.02 | 0.03 | 0.01 | 0.04 | 0.02 | 0.02 | 0.02 | 0.04 | 0.02 | 0.03 | 0.01 | 0.03 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.03 | 0.01 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.11 | 0.05 | 0.04 | 0.01 | 0.06 | 0.01 | 0.09 | 0.00 | 0.02 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.00 | 0.06 | 0.00 | 0.00 | 0.01 | 0.01 |
| SERPINE3 | ENSG00000253309 | 0.00 | 0.02 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.37 | 0.04 | 0.25 | 0.00 | 0.00 | 0.00 | 0.14 | 0.03 | 0.06 | 0.02 | 0.10 | 0.02 | 0.11 | 0.08 | 0.07 | 0.12 | 0.04 | 0.10 | 0.02 | 0.11 | 0.04 | 0.01 | 0.01 | 0.01 | 0.27 | 0.00 | 0.09 | 0.00 | 0.07 | 0.00 | 0.00 | 0.00 | 0.02 | 0.02 | 0.13 | 0.05 | 0.22 | 0.02 | 0.21 | 0.01 | 0.03 | 0.03 | 0.12 | 0.02 | 0.35 | 0.03 | 0.02 | 0.00 | 0.00 | 0.03 | 0.06 | 0.00 | 0.09 | 0.00 | 0.16 | 0.00 | 0.00 | 0.02 | 0.03 |
| HTR3C | ENSG00000178084 | 0.05 | 0.00 | 0.03 | 0.01 | 0.00 | 0.01 | 0.03 | 0.03 | 0.17 | 0.01 | 0.00 | 0.00 | 0.00 | 0.09 | 0.15 | 0.05 | 1.90 | 0.00 | 0.68 | 0.00 | 0.67 | 0.02 | 0.24 | 0.01 | 0.04 | 0.00 | 0.06 | 0.03 | 0.03 | 0.01 | 0.11 | 0.02 | 0.12 | 0.01 | 0.12 | 0.00 | 0.00 | 0.10 | 0.00 | 0.00 | 0.19 | 0.02 | 1.12 | 0.02 | 0.63 | 0.00 | 0.34 | 0.01 | 0.76 | 0.09 | 0.11 | 0.10 | 0.22 | 0.00 | 0.00 | 0.01 | 0.06 | 0.00 | 0.07 | 0.00 | 0.20 | 0.02 | 0.00 | 0.00 | 0.02 | 0.05 |
| GRM4 | ENSG00000124493 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.01 | 0.06 | 0.04 | 0.00 | 0.00 | 0.03 | 0.01 | 0.10 | 0.01 | 0.03 | 0.06 | 0.02 | 0.04 | 0.14 | 0.06 | 0.07 | 0.03 | 0.03 | 0.01 | 0.06 | 0.02 | 0.09 | 0.01 | 0.08 | 0.01 | 0.05 | 0.03 | 0.05 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.08 | 0.02 | 0.27 | 0.06 | 0.07 | 0.01 | 0.06 | 0.01 | 0.05 | 0.01 | 0.04 | 0.07 | 0.00 | 0.01 | 0.00 | 0.00 | 0.08 | 0.03 | 0.01 | 0.00 | 0.01 | 0.00 | 0.10 | 0.00 | 0.11 | 0.01 |
| IL1RAPL2 | ENSG00000189108 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.06 | 0.04 | 0.03 | 0.00 | 0.00 | 0.05 | 0.03 | 0.02 | 0.14 | 0.04 | 0.04 | 0.01 | 0.10 | 0.04 | 0.07 | 0.05 | 0.02 | 0.02 | 0.01 | 0.02 | 0.00 | 0.01 | 0.05 | 0.03 | 0.00 | 0.13 | 0.03 | 0.00 | 0.00 | 0.05 | 0.00 | 0.00 | 0.01 | 0.03 | 0.09 | 0.06 | 0.04 | 0.03 | 0.03 | 0.03 | 0.01 | 0.02 | 0.15 | 0.12 | 0.00 | 0.01 | 0.00 | 0.00 | 0.04 | 0.02 | 0.02 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 |
| COL6A6 | ENSG00000206384 | 0.02 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.04 | 0.03 | 0.04 | 0.02 | 0.00 | 0.01 | 0.00 | 0.03 | 0.04 | 0.02 | 0.15 | 0.01 | 0.08 | 0.00 | 0.17 | 0.02 | 0.06 | 0.02 | 0.01 | 0.00 | 0.02 | 0.01 | 0.02 | 0.00 | 0.03 | 0.01 | 0.00 | 0.05 | 0.06 | 0.02 | 0.00 | 0.06 | 0.00 | 0.00 | 0.05 | 0.03 | 0.29 | 0.04 | 0.11 | 0.00 | 0.07 | 0.00 | 0.18 | 0.03 | 0.04 | 0.06 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.02 | 0.00 | 0.02 | 0.01 | 0.05 | 0.00 | 0.00 | 0.02 | 0.05 |
| LIPF | ENSG00000182333 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.33 | 0.03 | 0.15 | 0.00 | 0.02 | 0.01 | 0.14 | 0.01 | 0.05 | 0.02 | 0.12 | 0.01 | 0.09 | 0.03 | 0.15 | 0.01 | 0.13 | 0.01 | 0.10 | 0.00 | 0.08 | 0.01 | 0.04 | 0.01 | 0.07 | 0.20 | 0.07 | 0.02 | 0.01 | 0.00 | 0.01 | 0.00 | 0.01 | 0.02 | 0.12 | 0.07 | 0.31 | 0.01 | 0.12 | 0.04 | 0.13 | 0.06 | 0.12 | 0.01 | 0.16 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.16 | 0.00 | 0.04 | 0.00 | 0.16 | 0.00 | 0.00 | 0.00 | 0.08 |
| PSKH2 | ENSG00000147613 | 0.00 | 0.00 | 0.00 | 0.01 | 0.06 | 0.00 | 0.06 | 0.02 | 0.15 | 0.01 | 0.00 | 0.00 | 0.02 | 0.00 | 0.15 | 0.01 | 0.13 | 0.03 | 0.06 | 0.01 | 0.16 | 0.00 | 0.15 | 0.00 | 0.10 | 0.00 | 0.12 | 0.03 | 0.02 | 0.01 | 0.15 | 0.00 | 0.20 | 0.01 | 0.06 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.29 | 0.01 | 0.31 | 0.11 | 0.06 | 0.01 | 0.06 | 0.02 | 0.23 | 0.04 | 0.20 | 0.05 | 0.16 | 0.00 | 0.00 | 0.00 | 0.04 | 0.02 | 0.03 | 0.00 | 0.01 | 0.01 | 0.25 | 0.00 | 0.10 | 0.01 |
| PRMT8 | ENSG00000111218 | 0.02 | 0.00 | 0.01 | 0.01 | 0.02 | 0.00 | 0.02 | 0.06 | 0.14 | 0.03 | 0.01 | 0.00 | 0.02 | 0.01 | 0.06 | 0.07 | 0.19 | 0.01 | 0.15 | 0.01 | 0.13 | 0.03 | 0.10 | 0.05 | 0.16 | 0.01 | 0.13 | 0.02 | 0.12 | 0.04 | 0.03 | 0.04 | 0.19 | 0.05 | 0.05 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.14 | 0.04 | 0.43 | 0.08 | 0.05 | 0.02 | 0.08 | 0.02 | 0.39 | 0.08 | 0.17 | 0.12 | 0.59 | 0.00 | 0.00 | 0.01 | 0.02 | 0.03 | 0.17 | 0.01 | 0.12 | 0.02 | 0.00 | 0.01 | 0.05 | 0.04 |
| MRGPRE | ENSG00000184350 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.03 | 0.00 | 0.02 | 0.01 | 0.10 | 0.00 | 0.00 | 0.02 | 0.05 | 0.02 | 0.06 | 0.01 | 0.16 | 0.01 | 0.07 | 0.02 | 0.14 | 0.01 | 0.06 | 0.01 | 0.01 | 0.01 | 0.03 | 0.00 | 0.06 | 0.04 | 0.04 | 0.03 | 0.01 | 0.01 | 0.05 | 0.02 | 0.07 | 0.00 | 0.00 | 0.02 | 0.12 | 0.02 | 0.46 | 0.01 | 0.06 | 0.03 | 0.07 | 0.03 | 0.09 | 0.04 | 0.15 | 0.02 | 0.02 | 0.00 | 0.00 | 0.05 | 0.00 | 0.01 | 0.10 | 0.01 | 0.05 | 0.00 | 0.00 | 0.01 | 0.04 |
| FGF6 | ENSG00000111241 | 0.01 | 0.00 | 0.00 | 0.01 | 0.02 | 0.00 | 0.01 | 0.06 | 0.09 | 0.03 | 0.01 | 0.00 | 0.02 | 0.01 | 0.06 | 0.07 | 0.18 | 0.01 | 0.15 | 0.01 | 0.11 | 0.03 | 0.06 | 0.06 | 0.17 | 0.01 | 0.15 | 0.02 | 0.10 | 0.05 | 0.02 | 0.04 | 0.14 | 0.05 | 0.07 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.14 | 0.04 | 0.37 | 0.08 | 0.05 | 0.02 | 0.07 | 0.02 | 0.34 | 0.02 | 0.24 | 0.11 | 0.57 | 0.00 | 0.00 | 0.01 | 0.02 | 0.03 | 0.20 | 0.00 | 0.15 | 0.01 | 0.00 | 0.01 | 0.05 | 0.04 |
| CST9L | ENSG00000101435 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.02 | 0.05 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.09 | 0.02 | 0.06 | 0.03 | 0.04 | 0.02 | 0.08 | 0.03 | 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 | 0.08 | 0.05 | 0.04 | 0.02 | 0.03 | 0.01 | 0.05 | 0.00 | 0.10 | 0.01 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.00 | 0.03 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.02 |
| TEX14 | ENSG00000121101 | 0.01 | 0.00 | 0.05 | 0.00 | 0.00 | 0.00 | 0.02 | 0.04 | 0.19 | 0.02 | 0.02 | 0.00 | 0.11 | 0.00 | 0.11 | 0.01 | 0.13 | 0.02 | 0.05 | 0.02 | 0.13 | 0.05 | 0.06 | 0.03 | 0.04 | 0.01 | 0.09 | 0.04 | 0.01 | 0.15 | 0.18 | 0.00 | 0.12 | 0.01 | 0.14 | 0.03 | 0.03 | 0.00 | 0.00 | 0.00 | 0.50 | 0.02 | 0.18 | 0.03 | 0.10 | 0.03 | 0.08 | 0.03 | 0.23 | 0.02 | 0.17 | 0.04 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.06 | 0.00 | 0.03 | 0.01 | 0.14 | 0.00 | 0.20 | 0.02 |
| HRH4 | ENSG00000134489 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.06 | 0.03 | 0.00 | 0.00 | 0.03 | 0.01 | 0.13 | 0.02 | 0.19 | 0.03 | 0.17 | 0.03 | 0.32 | 0.02 | 0.19 | 0.03 | 0.02 | 0.01 | 0.04 | 0.04 | 0.18 | 0.02 | 0.00 | 0.00 | 0.04 | 0.03 | 0.03 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.01 | 0.31 | 0.03 | 0.05 | 0.03 | 0.08 | 0.01 | 0.00 | 0.07 | 0.08 | 0.03 | 0.00 | 0.03 | 0.00 | 0.01 | 0.03 | 0.00 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 |
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