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 |
| IGHG2 | ENSG00000211893 | 0.00 | 0.02 | 0.01 | 0.01 | 0.01 | 0.04 | 0.02 | 0.03 | 0.08 | 0.07 | 0.00 | 0.00 | 0.00 | 0.07 | 0.06 | 0.07 | 0.20 | 0.03 | 0.07 | 0.05 | 0.09 | 0.08 | 0.03 | 0.07 | 0.01 | 0.03 | 0.03 | 0.04 | 0.02 | 0.02 | 0.01 | 0.14 | 0.04 | 0.31 | 0.16 | 0.00 | 0.01 | 0.03 | 0.00 | 0.00 | 0.07 | 0.07 | 0.37 | 0.17 | 0.07 | 0.08 | 0.09 | 0.02 | 0.07 | 0.05 | 0.14 | 0.06 | 0.03 | 0.01 | 0.00 | 0.00 | 0.08 | 0.03 | 0.01 | 0.07 | 0.02 | 0.05 | 0.03 | 0.03 | 0.01 | 0.07 |
| IGHG1 | ENSG00000211896 | 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 |
| IGHD | ENSG00000211898 | 0.00 | 0.02 | 0.01 | 0.01 | 0.01 | 0.04 | 0.02 | 0.03 | 0.08 | 0.07 | 0.00 | 0.00 | 0.00 | 0.07 | 0.06 | 0.07 | 0.20 | 0.03 | 0.07 | 0.05 | 0.09 | 0.08 | 0.03 | 0.07 | 0.01 | 0.03 | 0.03 | 0.04 | 0.02 | 0.02 | 0.01 | 0.14 | 0.04 | 0.31 | 0.16 | 0.00 | 0.01 | 0.03 | 0.00 | 0.00 | 0.07 | 0.07 | 0.37 | 0.17 | 0.07 | 0.08 | 0.09 | 0.02 | 0.07 | 0.05 | 0.14 | 0.06 | 0.03 | 0.01 | 0.00 | 0.00 | 0.08 | 0.03 | 0.01 | 0.07 | 0.02 | 0.05 | 0.03 | 0.03 | 0.01 | 0.07 |
| IGHM | ENSG00000211899 | 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 |
| IGHV1-2 | ENSG00000211934 | 0.00 | 0.02 | 0.01 | 0.01 | 0.01 | 0.04 | 0.02 | 0.03 | 0.08 | 0.07 | 0.00 | 0.00 | 0.00 | 0.07 | 0.06 | 0.07 | 0.20 | 0.03 | 0.07 | 0.05 | 0.09 | 0.08 | 0.03 | 0.07 | 0.01 | 0.03 | 0.03 | 0.04 | 0.02 | 0.02 | 0.01 | 0.14 | 0.04 | 0.31 | 0.16 | 0.00 | 0.01 | 0.03 | 0.00 | 0.00 | 0.07 | 0.07 | 0.37 | 0.17 | 0.07 | 0.08 | 0.09 | 0.02 | 0.07 | 0.05 | 0.14 | 0.06 | 0.03 | 0.01 | 0.00 | 0.00 | 0.08 | 0.03 | 0.01 | 0.07 | 0.02 | 0.05 | 0.03 | 0.03 | 0.01 | 0.07 |
| IGHV3-23 | ENSG00000211949 | 0.00 | 0.02 | 0.01 | 0.01 | 0.01 | 0.04 | 0.02 | 0.03 | 0.08 | 0.07 | 0.00 | 0.00 | 0.00 | 0.07 | 0.06 | 0.07 | 0.20 | 0.03 | 0.07 | 0.05 | 0.09 | 0.08 | 0.03 | 0.07 | 0.01 | 0.03 | 0.03 | 0.04 | 0.02 | 0.02 | 0.01 | 0.14 | 0.04 | 0.31 | 0.16 | 0.00 | 0.01 | 0.03 | 0.00 | 0.00 | 0.07 | 0.07 | 0.37 | 0.17 | 0.07 | 0.08 | 0.09 | 0.02 | 0.07 | 0.05 | 0.14 | 0.06 | 0.03 | 0.01 | 0.00 | 0.00 | 0.08 | 0.03 | 0.01 | 0.07 | 0.02 | 0.05 | 0.03 | 0.03 | 0.01 | 0.07 |
| IGHV1-46 | ENSG00000211962 | 0.00 | 0.02 | 0.01 | 0.01 | 0.01 | 0.04 | 0.02 | 0.03 | 0.08 | 0.07 | 0.00 | 0.00 | 0.00 | 0.07 | 0.06 | 0.07 | 0.20 | 0.03 | 0.07 | 0.05 | 0.09 | 0.08 | 0.03 | 0.07 | 0.01 | 0.03 | 0.03 | 0.04 | 0.02 | 0.02 | 0.01 | 0.14 | 0.04 | 0.31 | 0.16 | 0.00 | 0.01 | 0.03 | 0.00 | 0.00 | 0.07 | 0.07 | 0.37 | 0.17 | 0.07 | 0.08 | 0.09 | 0.02 | 0.07 | 0.05 | 0.14 | 0.06 | 0.03 | 0.01 | 0.00 | 0.00 | 0.08 | 0.03 | 0.01 | 0.07 | 0.02 | 0.05 | 0.03 | 0.03 | 0.01 | 0.07 |
| TSSK1B | ENSG00000212122 | 0.19 | 0.01 | 0.03 | 0.01 | 0.00 | 0.01 | 0.03 | 0.13 | 0.03 | 0.09 | 0.00 | 0.01 | 0.00 | 0.08 | 0.02 | 0.07 | 0.00 | 0.09 | 0.00 | 0.06 | 0.03 | 0.09 | 0.02 | 0.13 | 0.01 | 0.14 | 0.01 | 0.11 | 0.01 | 0.03 | 0.07 | 0.04 | 0.00 | 0.02 | 0.26 | 0.04 | 0.01 | 0.03 | 0.00 | 0.00 | 0.02 | 0.06 | 0.09 | 0.37 | 0.00 | 0.06 | 0.01 | 0.03 | 0.01 | 0.07 | 0.07 | 0.04 | 0.01 | 0.00 | 0.00 | 0.09 | 0.04 | 0.02 | 0.01 | 0.02 | 0.01 | 0.01 | 0.00 | 0.00 | 0.05 | 0.06 |
| TAS2R19 | ENSG00000212124 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.16 | 0.04 | 0.08 | 0.01 | 0.00 | 0.00 | 0.05 | 0.04 | 0.10 | 0.12 | 0.01 | 0.10 | 0.03 | 0.05 | 0.04 | 0.03 | 0.08 | 0.01 | 0.03 | 0.03 | 0.03 | 0.01 | 0.06 | 0.00 | 0.06 | 0.14 | 0.05 | 0.03 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.10 | 0.06 | 0.33 | 0.10 | 0.01 | 0.02 | 0.03 | 0.03 | 0.04 | 0.03 | 0.12 | 0.16 | 0.55 | 0.00 | 0.00 | 0.03 | 0.00 | 0.04 | 0.09 | 0.01 | 0.01 | 0.05 | 0.00 | 0.01 | 0.04 | 0.03 |
| TAS2R50 | ENSG00000212126 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.16 | 0.04 | 0.08 | 0.01 | 0.00 | 0.00 | 0.05 | 0.04 | 0.10 | 0.12 | 0.01 | 0.10 | 0.03 | 0.05 | 0.04 | 0.03 | 0.08 | 0.01 | 0.03 | 0.03 | 0.03 | 0.01 | 0.06 | 0.00 | 0.06 | 0.14 | 0.05 | 0.03 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.10 | 0.06 | 0.32 | 0.10 | 0.02 | 0.02 | 0.03 | 0.03 | 0.04 | 0.03 | 0.13 | 0.16 | 0.55 | 0.00 | 0.00 | 0.03 | 0.00 | 0.04 | 0.09 | 0.01 | 0.02 | 0.05 | 0.00 | 0.01 | 0.04 | 0.03 |
| TAS2R14 | ENSG00000212127 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.16 | 0.04 | 0.08 | 0.01 | 0.00 | 0.00 | 0.05 | 0.04 | 0.10 | 0.12 | 0.01 | 0.10 | 0.03 | 0.05 | 0.04 | 0.03 | 0.08 | 0.01 | 0.03 | 0.03 | 0.03 | 0.01 | 0.06 | 0.00 | 0.06 | 0.14 | 0.05 | 0.03 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.10 | 0.06 | 0.34 | 0.10 | 0.02 | 0.02 | 0.03 | 0.03 | 0.04 | 0.03 | 0.13 | 0.16 | 0.55 | 0.00 | 0.00 | 0.03 | 0.00 | 0.04 | 0.09 | 0.01 | 0.02 | 0.05 | 0.00 | 0.01 | 0.04 | 0.03 |
| TAS2R13 | ENSG00000212128 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.15 | 0.04 | 0.08 | 0.01 | 0.00 | 0.00 | 0.05 | 0.04 | 0.10 | 0.13 | 0.01 | 0.10 | 0.03 | 0.05 | 0.04 | 0.03 | 0.08 | 0.01 | 0.03 | 0.03 | 0.03 | 0.01 | 0.06 | 0.00 | 0.06 | 0.14 | 0.05 | 0.03 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.10 | 0.06 | 0.32 | 0.10 | 0.02 | 0.02 | 0.03 | 0.03 | 0.04 | 0.03 | 0.13 | 0.15 | 0.55 | 0.00 | 0.00 | 0.03 | 0.00 | 0.04 | 0.09 | 0.01 | 0.03 | 0.05 | 0.00 | 0.01 | 0.04 | 0.03 |
| OR2A42 | ENSG00000212807 | 0.03 | 0.01 | 0.05 | 0.00 | 0.05 | 0.02 | 0.03 | 0.03 | 0.05 | 0.04 | 0.00 | 0.01 | 0.04 | 0.03 | 0.08 | 0.02 | 0.09 | 0.07 | 0.02 | 0.16 | 0.04 | 0.22 | 0.02 | 0.10 | 0.02 | 0.01 | 0.01 | 0.02 | 0.02 | 0.04 | 0.04 | 0.05 | 0.00 | 0.11 | 0.06 | 0.06 | 0.00 | 0.02 | 0.00 | 0.00 | 0.09 | 0.05 | 0.53 | 0.05 | 0.03 | 0.09 | 0.04 | 0.05 | 0.07 | 0.14 | 0.12 | 0.13 | 0.02 | 0.04 | 0.00 | 0.06 | 0.02 | 0.09 | 0.10 | 0.01 | 0.04 | 0.02 | 0.00 | 0.03 | 0.21 | 0.02 |
| KLK9 | ENSG00000213022 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.02 | 0.00 | 0.13 | 0.04 | 0.00 | 0.00 | 0.00 | 0.06 | 0.02 | 0.08 | 0.07 | 0.10 | 0.03 | 0.02 | 0.07 | 0.03 | 0.09 | 0.03 | 0.02 | 0.02 | 0.02 | 0.04 | 0.04 | 0.04 | 0.05 | 0.03 | 0.00 | 0.07 | 0.23 | 0.02 | 0.00 | 0.03 | 0.00 | 0.00 | 0.12 | 0.04 | 0.10 | 0.31 | 0.07 | 0.07 | 0.04 | 0.05 | 0.24 | 0.13 | 0.03 | 0.17 | 0.00 | 0.04 | 0.01 | 0.00 | 0.13 | 0.03 | 0.01 | 0.16 | 0.01 | 0.14 | 0.00 | 0.00 | 0.03 | 0.03 |
| CGB8 | ENSG00000213030 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.03 | 0.08 | 0.04 | 0.00 | 0.02 | 0.00 | 0.06 | 0.01 | 0.07 | 0.04 | 0.10 | 0.03 | 0.02 | 0.08 | 0.05 | 0.06 | 0.03 | 0.01 | 0.03 | 0.01 | 0.03 | 0.03 | 0.05 | 0.04 | 0.03 | 0.00 | 0.07 | 0.17 | 0.02 | 0.00 | 0.03 | 0.00 | 0.00 | 0.08 | 0.05 | 0.05 | 0.31 | 0.05 | 0.07 | 0.03 | 0.05 | 0.17 | 0.19 | 0.04 | 0.18 | 0.00 | 0.04 | 0.01 | 0.00 | 0.07 | 0.05 | 0.00 | 0.14 | 0.01 | 0.13 | 0.00 | 0.00 | 0.02 | 0.02 |
| ACKR1 | ENSG00000213088 | 0.03 | 0.00 | 0.01 | 0.01 | 0.00 | 0.03 | 0.02 | 0.05 | 0.53 | 0.01 | 0.02 | 0.00 | 0.11 | 0.00 | 0.27 | 0.00 | 0.25 | 0.01 | 0.06 | 0.00 | 0.25 | 0.00 | 0.12 | 0.00 | 0.03 | 0.00 | 0.11 | 0.00 | 0.06 | 0.00 | 0.28 | 0.00 | 0.30 | 0.01 | 0.16 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.24 | 0.01 | 0.38 | 0.02 | 0.16 | 0.00 | 0.13 | 0.00 | 0.28 | 0.00 | 0.36 | 0.02 | 0.10 | 0.00 | 0.00 | 0.00 | 0.24 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.16 | 0.01 |
| KLHL23 | ENSG00000213160 | 0.02 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.01 | 0.10 | 0.06 | 0.04 | 0.00 | 0.01 | 0.00 | 0.00 | 0.07 | 0.01 | 0.10 | 0.02 | 0.09 | 0.01 | 0.10 | 0.02 | 0.04 | 0.04 | 0.01 | 0.01 | 0.03 | 0.02 | 0.03 | 0.01 | 0.06 | 0.06 | 0.00 | 0.01 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.03 | 0.30 | 0.06 | 0.08 | 0.01 | 0.04 | 0.01 | 0.06 | 0.04 | 0.04 | 0.09 | 0.04 | 0.00 | 0.00 | 0.01 | 0.00 | 0.07 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.02 |
| ASIC3 | ENSG00000213199 | 0.03 | 0.01 | 0.04 | 0.00 | 0.09 | 0.00 | 0.03 | 0.03 | 0.05 | 0.05 | 0.00 | 0.01 | 0.00 | 0.03 | 0.10 | 0.02 | 0.10 | 0.09 | 0.02 | 0.17 | 0.04 | 0.25 | 0.03 | 0.10 | 0.02 | 0.01 | 0.01 | 0.02 | 0.02 | 0.05 | 0.07 | 0.04 | 0.00 | 0.11 | 0.07 | 0.07 | 0.00 | 0.03 | 0.00 | 0.00 | 0.07 | 0.07 | 0.53 | 0.08 | 0.04 | 0.09 | 0.03 | 0.06 | 0.08 | 0.19 | 0.10 | 0.15 | 0.01 | 0.05 | 0.00 | 0.06 | 0.02 | 0.09 | 0.10 | 0.01 | 0.07 | 0.01 | 0.00 | 0.03 | 0.20 | 0.03 |
| OR2F1 | ENSG00000213215 | 0.02 | 0.01 | 0.05 | 0.00 | 0.05 | 0.02 | 0.02 | 0.03 | 0.05 | 0.03 | 0.00 | 0.01 | 0.04 | 0.05 | 0.07 | 0.02 | 0.09 | 0.07 | 0.02 | 0.15 | 0.03 | 0.21 | 0.03 | 0.09 | 0.04 | 0.00 | 0.01 | 0.02 | 0.02 | 0.04 | 0.05 | 0.05 | 0.00 | 0.11 | 0.06 | 0.06 | 0.00 | 0.02 | 0.01 | 0.00 | 0.08 | 0.05 | 0.53 | 0.05 | 0.03 | 0.09 | 0.04 | 0.05 | 0.05 | 0.14 | 0.13 | 0.12 | 0.02 | 0.04 | 0.00 | 0.05 | 0.02 | 0.09 | 0.10 | 0.01 | 0.04 | 0.02 | 0.00 | 0.03 | 0.20 | 0.02 |
| CSH2 | ENSG00000213218 | 0.02 | 0.00 | 0.05 | 0.00 | 0.00 | 0.00 | 0.03 | 0.02 | 0.26 | 0.01 | 0.02 | 0.00 | 0.12 | 0.00 | 0.14 | 0.01 | 0.20 | 0.01 | 0.07 | 0.02 | 0.21 | 0.02 | 0.11 | 0.02 | 0.07 | 0.01 | 0.07 | 0.02 | 0.08 | 0.10 | 0.20 | 0.00 | 0.12 | 0.01 | 0.15 | 0.03 | 0.02 | 0.00 | 0.00 | 0.00 | 0.56 | 0.01 | 0.24 | 0.03 | 0.17 | 0.02 | 0.10 | 0.03 | 0.27 | 0.02 | 0.17 | 0.03 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.02 | 0.06 | 0.00 | 0.03 | 0.01 | 0.16 | 0.00 | 0.24 | 0.01 |
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