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 |
| DDC | ENSG00000132437 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.09 | 0.01 | 0.00 | 0.00 | 0.02 | 0.00 | 0.10 | 0.01 | 0.13 | 0.03 | 0.10 | 0.01 | 0.10 | 0.04 | 0.05 | 0.01 | 0.02 | 0.00 | 0.02 | 0.00 | 0.02 | 0.00 | 0.02 | 0.00 | 0.06 | 0.01 | 0.07 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.03 | 0.09 | 0.04 | 0.01 | 0.01 | 0.02 | 0.02 | 0.01 | 0.00 | 0.05 | 0.02 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.05 | 0.02 | 0.00 | 0.12 | 0.01 | 0.00 | 0.00 | 0.03 | 0.03 |
| ENAM | ENSG00000132464 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.02 | 0.13 | 0.03 | 0.00 | 0.00 | 0.00 | 0.06 | 0.07 | 0.03 | 0.20 | 0.01 | 0.08 | 0.01 | 0.11 | 0.04 | 0.05 | 0.03 | 0.01 | 0.01 | 0.03 | 0.01 | 0.00 | 0.01 | 0.01 | 0.07 | 0.00 | 0.03 | 0.06 | 0.00 | 0.02 | 0.02 | 0.00 | 0.00 | 0.11 | 0.02 | 0.24 | 0.09 | 0.04 | 0.04 | 0.04 | 0.01 | 0.15 | 0.05 | 0.07 | 0.05 | 0.10 | 0.00 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.02 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.03 |
| JCHAIN | ENSG00000132465 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.02 | 0.13 | 0.03 | 0.00 | 0.00 | 0.00 | 0.06 | 0.07 | 0.03 | 0.20 | 0.01 | 0.08 | 0.01 | 0.11 | 0.04 | 0.05 | 0.03 | 0.01 | 0.01 | 0.03 | 0.01 | 0.00 | 0.01 | 0.01 | 0.07 | 0.00 | 0.03 | 0.06 | 0.00 | 0.02 | 0.02 | 0.00 | 0.00 | 0.11 | 0.02 | 0.24 | 0.09 | 0.04 | 0.04 | 0.04 | 0.01 | 0.15 | 0.05 | 0.07 | 0.05 | 0.10 | 0.00 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.02 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.03 |
| H3F3B | ENSG00000132475 | 0.02 | 0.00 | 0.05 | 0.00 | 0.02 | 0.00 | 0.04 | 0.03 | 0.21 | 0.00 | 0.00 | 0.01 | 0.09 | 0.02 | 0.15 | 0.02 | 0.26 | 0.01 | 0.10 | 0.03 | 0.23 | 0.07 | 0.10 | 0.04 | 0.05 | 0.01 | 0.06 | 0.03 | 0.04 | 0.10 | 0.26 | 0.00 | 0.08 | 0.01 | 0.14 | 0.02 | 0.02 | 0.01 | 0.00 | 0.00 | 0.37 | 0.03 | 0.35 | 0.05 | 0.24 | 0.02 | 0.22 | 0.01 | 0.71 | 0.00 | 0.25 | 0.02 | 0.04 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.09 | 0.00 | 0.07 | 0.01 | 0.14 | 0.01 | 0.24 | 0.02 |
| CLEC10A | ENSG00000132514 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.20 | 0.05 | 0.03 | 0.00 | 0.02 | 0.00 | 0.02 | 0.01 | 0.05 | 0.01 | 0.02 | 0.01 | 0.03 | 0.03 | 0.04 | 0.02 | 0.02 | 0.00 | 0.02 | 0.00 | 0.03 | 0.02 | 0.03 | 0.00 | 0.14 | 0.00 | 0.11 | 0.02 | 0.08 | 0.00 | 0.03 | 0.00 | 0.00 | 0.01 | 0.07 | 0.10 | 0.04 | 0.01 | 0.03 | 0.04 | 0.03 | 0.06 | 0.18 | 0.07 | 0.34 | 0.00 | 0.02 | 0.01 | 0.02 | 0.00 | 0.06 | 0.00 | 0.01 | 0.00 | 0.07 | 0.00 | 0.00 | 0.02 | 0.04 |
| GUCY2D | ENSG00000132518 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.22 | 0.02 | 0.03 | 0.00 | 0.01 | 0.00 | 0.03 | 0.01 | 0.05 | 0.01 | 0.02 | 0.01 | 0.03 | 0.03 | 0.04 | 0.01 | 0.02 | 0.00 | 0.02 | 0.00 | 0.02 | 0.01 | 0.02 | 0.00 | 0.16 | 0.02 | 0.08 | 0.01 | 0.05 | 0.00 | 0.03 | 0.00 | 0.00 | 0.01 | 0.06 | 0.09 | 0.05 | 0.00 | 0.04 | 0.03 | 0.04 | 0.06 | 0.15 | 0.19 | 0.31 | 0.00 | 0.02 | 0.02 | 0.01 | 0.00 | 0.10 | 0.01 | 0.00 | 0.00 | 0.06 | 0.00 | 0.00 | 0.01 | 0.04 |
| SDF2 | ENSG00000132581 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.01 | 0.25 | 0.01 | 0.08 | 0.00 | 0.00 | 0.03 | 0.07 | 0.01 | 0.10 | 0.03 | 0.05 | 0.02 | 0.18 | 0.01 | 0.12 | 0.00 | 0.11 | 0.01 | 0.07 | 0.01 | 0.03 | 0.01 | 0.05 | 0.00 | 0.07 | 0.01 | 0.02 | 0.04 | 0.00 | 0.14 | 0.00 | 0.00 | 0.34 | 0.03 | 0.18 | 0.07 | 0.02 | 0.03 | 0.17 | 0.02 | 0.22 | 0.05 | 0.04 | 0.17 | 0.00 | 0.01 | 0.00 | 0.02 | 0.04 | 0.00 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.04 | 0.03 |
| SNAP25 | ENSG00000132639 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.01 | 0.01 | 0.03 | 0.02 | 0.00 | 0.00 | 0.00 | 0.03 | 0.04 | 0.04 | 0.14 | 0.02 | 0.11 | 0.02 | 0.07 | 0.01 | 0.04 | 0.02 | 0.06 | 0.04 | 0.06 | 0.07 | 0.00 | 0.01 | 0.03 | 0.01 | 0.00 | 0.03 | 0.04 | 0.07 | 0.00 | 0.01 | 0.00 | 0.00 | 0.04 | 0.05 | 0.19 | 0.07 | 0.04 | 0.01 | 0.05 | 0.01 | 0.03 | 0.09 | 0.07 | 0.05 | 0.00 | 0.02 | 0.00 | 0.01 | 0.01 | 0.02 | 0.01 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.02 | 0.02 |
| SSTR4 | ENSG00000132671 | 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 | 0.03 | 0.09 | 0.01 | 0.06 | 0.03 | 0.05 | 0.02 | 0.07 | 0.03 | 0.06 | 0.01 | 0.04 | 0.01 | 0.03 | 0.02 | 0.06 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.06 | 0.03 | 0.08 | 0.05 | 0.04 | 0.02 | 0.02 | 0.01 | 0.05 | 0.00 | 0.07 | 0.02 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 |
| RHBG | ENSG00000132677 | 0.03 | 0.00 | 0.01 | 0.00 | 0.00 | 0.03 | 0.02 | 0.03 | 0.33 | 0.01 | 0.02 | 0.00 | 0.11 | 0.00 | 0.32 | 0.00 | 0.23 | 0.00 | 0.05 | 0.01 | 0.24 | 0.00 | 0.14 | 0.00 | 0.03 | 0.00 | 0.11 | 0.00 | 0.07 | 0.00 | 0.32 | 0.00 | 0.48 | 0.01 | 0.09 | 0.02 | 0.06 | 0.00 | 0.00 | 0.00 | 0.28 | 0.01 | 0.50 | 0.02 | 0.18 | 0.00 | 0.22 | 0.00 | 0.59 | 0.01 | 0.34 | 0.01 | 0.10 | 0.00 | 0.00 | 0.00 | 0.25 | 0.00 | 0.05 | 0.00 | 0.08 | 0.00 | 0.00 | 0.00 | 0.17 | 0.01 |
| CRP | ENSG00000132693 | 0.03 | 0.00 | 0.01 | 0.01 | 0.00 | 0.03 | 0.02 | 0.04 | 0.64 | 0.00 | 0.02 | 0.00 | 0.10 | 0.00 | 0.28 | 0.00 | 0.27 | 0.00 | 0.06 | 0.00 | 0.27 | 0.00 | 0.12 | 0.00 | 0.03 | 0.00 | 0.13 | 0.00 | 0.06 | 0.00 | 0.29 | 0.00 | 0.30 | 0.01 | 0.16 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.27 | 0.01 | 0.40 | 0.02 | 0.16 | 0.00 | 0.13 | 0.00 | 0.28 | 0.00 | 0.42 | 0.02 | 0.10 | 0.00 | 0.00 | 0.00 | 0.24 | 0.00 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.16 | 0.01 |
| APCS | ENSG00000132703 | 0.03 | 0.00 | 0.01 | 0.01 | 0.00 | 0.03 | 0.02 | 0.04 | 0.60 | 0.00 | 0.02 | 0.00 | 0.11 | 0.00 | 0.27 | 0.00 | 0.25 | 0.00 | 0.05 | 0.00 | 0.27 | 0.00 | 0.12 | 0.00 | 0.03 | 0.00 | 0.11 | 0.00 | 0.06 | 0.00 | 0.30 | 0.00 | 0.30 | 0.01 | 0.16 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.26 | 0.01 | 0.38 | 0.02 | 0.17 | 0.00 | 0.14 | 0.00 | 0.28 | 0.00 | 0.37 | 0.03 | 0.10 | 0.00 | 0.00 | 0.00 | 0.24 | 0.00 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.16 | 0.01 |
| FCRL2 | ENSG00000132704 | 0.03 | 0.00 | 0.01 | 0.01 | 0.00 | 0.03 | 0.02 | 0.07 | 0.39 | 0.01 | 0.02 | 0.00 | 0.11 | 0.00 | 0.26 | 0.00 | 0.25 | 0.01 | 0.07 | 0.00 | 0.25 | 0.00 | 0.12 | 0.00 | 0.03 | 0.00 | 0.11 | 0.00 | 0.07 | 0.00 | 0.30 | 0.00 | 0.41 | 0.01 | 0.05 | 0.02 | 0.04 | 0.00 | 0.00 | 0.00 | 0.27 | 0.01 | 0.39 | 0.02 | 0.15 | 0.00 | 0.15 | 0.00 | 0.37 | 0.00 | 0.38 | 0.01 | 0.10 | 0.00 | 0.00 | 0.00 | 0.25 | 0.00 | 0.01 | 0.00 | 0.05 | 0.00 | 0.00 | 0.03 | 0.18 | 0.01 |
| BHMT2 | ENSG00000132840 | 0.01 | 0.01 | 0.01 | 0.01 | 0.03 | 0.01 | 0.00 | 0.16 | 0.02 | 0.11 | 0.00 | 0.01 | 0.00 | 0.03 | 0.01 | 0.08 | 0.00 | 0.09 | 0.01 | 0.08 | 0.02 | 0.13 | 0.00 | 0.12 | 0.01 | 0.05 | 0.01 | 0.05 | 0.00 | 0.07 | 0.01 | 0.04 | 0.00 | 0.08 | 0.09 | 0.03 | 0.02 | 0.04 | 0.00 | 0.00 | 0.01 | 0.09 | 0.02 | 0.67 | 0.00 | 0.05 | 0.00 | 0.09 | 0.00 | 0.25 | 0.04 | 0.04 | 0.01 | 0.00 | 0.00 | 0.02 | 0.02 | 0.00 | 0.01 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.06 | 0.03 |
| ANGPTL3 | ENSG00000132855 | 0.00 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.06 | 0.07 | 0.05 | 0.00 | 0.02 | 0.04 | 0.01 | 0.06 | 0.06 | 0.07 | 0.04 | 0.05 | 0.03 | 0.08 | 0.05 | 0.03 | 0.04 | 0.00 | 0.06 | 0.00 | 0.05 | 0.00 | 0.01 | 0.02 | 0.05 | 0.00 | 0.13 | 0.04 | 0.03 | 0.01 | 0.17 | 0.00 | 0.00 | 0.10 | 0.06 | 0.20 | 0.13 | 0.09 | 0.02 | 0.04 | 0.02 | 0.00 | 0.06 | 0.24 | 0.03 | 0.03 | 0.05 | 0.02 | 0.01 | 0.00 | 0.03 | 0.00 | 0.01 | 0.02 | 0.01 | 0.00 | 0.07 | 0.04 | 0.03 |
| NMUR2 | ENSG00000132911 | 0.30 | 0.00 | 0.04 | 0.01 | 0.00 | 0.00 | 0.02 | 0.02 | 0.01 | 0.05 | 0.00 | 0.00 | 0.02 | 0.03 | 0.04 | 0.04 | 0.01 | 0.03 | 0.01 | 0.05 | 0.04 | 0.01 | 0.04 | 0.04 | 0.01 | 0.02 | 0.04 | 0.01 | 0.02 | 0.02 | 0.09 | 0.02 | 0.09 | 0.01 | 0.31 | 0.04 | 0.00 | 0.03 | 0.01 | 0.00 | 0.04 | 0.03 | 0.16 | 0.11 | 0.03 | 0.03 | 0.02 | 0.02 | 0.05 | 0.02 | 0.08 | 0.07 | 0.00 | 0.00 | 0.00 | 0.09 | 0.04 | 0.00 | 0.00 | 0.07 | 0.01 | 0.04 | 0.03 | 0.03 | 0.04 | 0.14 |
| PDE6A | ENSG00000132915 | 0.31 | 0.00 | 0.02 | 0.01 | 0.05 | 0.00 | 0.02 | 0.01 | 0.03 | 0.05 | 0.00 | 0.00 | 0.02 | 0.05 | 0.04 | 0.04 | 0.01 | 0.03 | 0.01 | 0.04 | 0.05 | 0.02 | 0.03 | 0.04 | 0.01 | 0.01 | 0.04 | 0.01 | 0.03 | 0.02 | 0.11 | 0.02 | 0.09 | 0.01 | 0.26 | 0.04 | 0.00 | 0.03 | 0.01 | 0.00 | 0.04 | 0.02 | 0.19 | 0.09 | 0.03 | 0.02 | 0.04 | 0.02 | 0.13 | 0.02 | 0.06 | 0.05 | 0.00 | 0.00 | 0.00 | 0.10 | 0.06 | 0.00 | 0.00 | 0.06 | 0.01 | 0.03 | 0.00 | 0.03 | 0.05 | 0.14 |
| RNF17 | ENSG00000132972 | 0.02 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.04 | 0.09 | 0.05 | 0.00 | 0.02 | 0.00 | 0.17 | 0.01 | 0.11 | 0.02 | 0.12 | 0.02 | 0.15 | 0.05 | 0.09 | 0.07 | 0.04 | 0.23 | 0.00 | 0.23 | 0.02 | 0.00 | 0.00 | 0.03 | 0.12 | 0.00 | 0.15 | 0.00 | 0.09 | 0.00 | 0.00 | 0.00 | 0.01 | 0.08 | 0.08 | 0.10 | 0.19 | 0.03 | 0.14 | 0.02 | 0.05 | 0.01 | 0.16 | 0.13 | 0.19 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.09 | 0.01 | 0.06 | 0.01 | 0.06 | 0.00 | 0.00 | 0.05 | 0.03 |
| GPR12 | ENSG00000132975 | 0.01 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.02 | 0.11 | 0.04 | 0.00 | 0.02 | 0.00 | 0.18 | 0.03 | 0.09 | 0.03 | 0.11 | 0.03 | 0.13 | 0.08 | 0.09 | 0.09 | 0.04 | 0.29 | 0.00 | 0.39 | 0.02 | 0.00 | 0.00 | 0.03 | 0.11 | 0.00 | 0.15 | 0.00 | 0.09 | 0.00 | 0.00 | 0.00 | 0.01 | 0.10 | 0.06 | 0.07 | 0.18 | 0.03 | 0.13 | 0.01 | 0.05 | 0.01 | 0.16 | 0.12 | 0.23 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.09 | 0.01 | 0.06 | 0.01 | 0.06 | 0.00 | 0.00 | 0.06 | 0.03 |
| PIK3C2B | ENSG00000133056 | 0.04 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.03 | 0.00 | 0.07 | 0.06 | 0.02 | 0.00 | 0.12 | 0.00 | 0.15 | 0.00 | 0.12 | 0.01 | 0.05 | 0.00 | 0.19 | 0.06 | 0.07 | 0.02 | 0.04 | 0.01 | 0.13 | 0.01 | 0.00 | 0.00 | 0.19 | 0.01 | 0.18 | 0.02 | 0.06 | 0.02 | 0.02 | 0.00 | 0.00 | 0.00 | 0.28 | 0.00 | 0.32 | 0.08 | 0.06 | 0.01 | 0.15 | 0.01 | 0.20 | 0.00 | 0.16 | 0.13 | 0.06 | 0.00 | 0.01 | 0.00 | 0.26 | 0.02 | 0.22 | 0.00 | 0.73 | 0.00 | 0.09 | 0.00 | 0.22 | 0.01 |
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