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 |
| VCAM1 | ENSG00000162692 | 0.00 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.07 | 0.03 | 0.07 | 0.00 | 0.00 | 0.00 | 0.38 | 0.02 | 0.12 | 0.02 | 0.09 | 0.01 | 0.08 | 0.02 | 0.10 | 0.01 | 0.06 | 0.00 | 0.07 | 0.01 | 0.06 | 0.00 | 0.02 | 0.04 | 0.04 | 0.00 | 0.11 | 0.04 | 0.04 | 0.00 | 0.25 | 0.00 | 0.00 | 0.02 | 0.11 | 0.14 | 0.18 | 0.00 | 0.07 | 0.02 | 0.02 | 0.01 | 0.06 | 0.06 | 0.09 | 0.03 | 0.05 | 0.00 | 0.00 | 0.00 | 0.07 | 0.01 | 0.01 | 0.01 | 0.03 | 0.00 | 0.03 | 0.05 | 0.10 |
| EXTL2 | ENSG00000162694 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.07 | 0.02 | 0.07 | 0.00 | 0.00 | 0.00 | 0.38 | 0.02 | 0.12 | 0.02 | 0.10 | 0.01 | 0.08 | 0.02 | 0.10 | 0.01 | 0.06 | 0.00 | 0.07 | 0.01 | 0.06 | 0.00 | 0.02 | 0.03 | 0.04 | 0.00 | 0.11 | 0.04 | 0.04 | 0.00 | 0.25 | 0.00 | 0.00 | 0.01 | 0.11 | 0.14 | 0.17 | 0.00 | 0.07 | 0.02 | 0.02 | 0.01 | 0.06 | 0.06 | 0.09 | 0.03 | 0.05 | 0.00 | 0.00 | 0.00 | 0.07 | 0.01 | 0.01 | 0.01 | 0.03 | 0.00 | 0.03 | 0.03 | 0.11 |
| SLC30A7 | ENSG00000162695 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.07 | 0.02 | 0.07 | 0.00 | 0.00 | 0.00 | 0.38 | 0.02 | 0.12 | 0.02 | 0.10 | 0.01 | 0.08 | 0.02 | 0.10 | 0.01 | 0.06 | 0.00 | 0.07 | 0.01 | 0.06 | 0.00 | 0.02 | 0.03 | 0.04 | 0.00 | 0.11 | 0.04 | 0.04 | 0.00 | 0.25 | 0.00 | 0.00 | 0.02 | 0.11 | 0.14 | 0.18 | 0.00 | 0.07 | 0.02 | 0.02 | 0.01 | 0.06 | 0.06 | 0.09 | 0.03 | 0.05 | 0.00 | 0.00 | 0.00 | 0.07 | 0.01 | 0.01 | 0.01 | 0.03 | 0.00 | 0.03 | 0.03 | 0.11 |
| OR2M5 | ENSG00000162727 | 0.01 | 0.02 | 0.01 | 0.01 | 0.00 | 0.01 | 0.02 | 0.04 | 0.14 | 0.04 | 0.02 | 0.02 | 0.08 | 0.05 | 0.13 | 0.01 | 0.17 | 0.03 | 0.10 | 0.02 | 0.27 | 0.04 | 0.13 | 0.01 | 0.04 | 0.02 | 0.08 | 0.01 | 0.02 | 0.01 | 0.20 | 0.02 | 0.23 | 0.02 | 0.10 | 0.07 | 0.00 | 0.04 | 0.00 | 0.00 | 0.29 | 0.02 | 0.48 | 0.12 | 0.13 | 0.01 | 0.12 | 0.02 | 0.32 | 0.00 | 0.09 | 0.24 | 0.06 | 0.02 | 0.01 | 0.00 | 0.03 | 0.18 | 0.02 | 0.04 | 0.02 | 0.04 | 0.15 | 0.03 | 0.24 | 0.02 |
| KCNJ9 | ENSG00000162728 | 0.03 | 0.00 | 0.01 | 0.01 | 0.00 | 0.03 | 0.02 | 0.04 | 0.76 | 0.00 | 0.02 | 0.00 | 0.10 | 0.01 | 0.28 | 0.00 | 0.28 | 0.00 | 0.06 | 0.00 | 0.27 | 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 | 0.28 | 0.01 | 0.42 | 0.02 | 0.16 | 0.00 | 0.15 | 0.00 | 0.28 | 0.00 | 0.49 | 0.02 | 0.10 | 0.00 | 0.00 | 0.00 | 0.24 | 0.00 | 0.02 | 0.00 | 0.05 | 0.00 | 0.00 | 0.00 | 0.16 | 0.00 |
| SLAMF6 | ENSG00000162739 | 0.03 | 0.00 | 0.01 | 0.01 | 0.00 | 0.03 | 0.02 | 0.04 | 0.76 | 0.00 | 0.02 | 0.00 | 0.10 | 0.02 | 0.27 | 0.00 | 0.28 | 0.00 | 0.06 | 0.00 | 0.27 | 0.00 | 0.14 | 0.00 | 0.03 | 0.00 | 0.11 | 0.00 | 0.06 | 0.00 | 0.28 | 0.00 | 0.30 | 0.00 | 0.16 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.29 | 0.01 | 0.40 | 0.02 | 0.16 | 0.00 | 0.14 | 0.00 | 0.28 | 0.00 | 0.48 | 0.02 | 0.10 | 0.00 | 0.00 | 0.00 | 0.24 | 0.06 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.18 | 0.01 |
| OLFML2B | ENSG00000162745 | 0.03 | 0.00 | 0.01 | 0.01 | 0.00 | 0.03 | 0.01 | 0.04 | 0.82 | 0.01 | 0.02 | 0.00 | 0.10 | 0.01 | 0.25 | 0.00 | 0.27 | 0.00 | 0.05 | 0.00 | 0.25 | 0.01 | 0.13 | 0.01 | 0.03 | 0.00 | 0.14 | 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 | 0.30 | 0.01 | 0.37 | 0.02 | 0.15 | 0.00 | 0.12 | 0.00 | 0.33 | 0.00 | 0.36 | 0.03 | 0.10 | 0.00 | 0.00 | 0.00 | 0.25 | 0.00 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.18 | 0.01 |
| FCGR3B | ENSG00000162747 | 0.03 | 0.00 | 0.01 | 0.01 | 0.00 | 0.03 | 0.02 | 0.04 | 0.79 | 0.01 | 0.02 | 0.00 | 0.10 | 0.01 | 0.27 | 0.00 | 0.27 | 0.00 | 0.05 | 0.00 | 0.29 | 0.01 | 0.13 | 0.00 | 0.03 | 0.00 | 0.14 | 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 | 0.31 | 0.01 | 0.37 | 0.02 | 0.17 | 0.00 | 0.13 | 0.00 | 0.28 | 0.00 | 0.34 | 0.03 | 0.10 | 0.00 | 0.00 | 0.00 | 0.25 | 0.00 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.18 | 0.01 |
| FLVCR1 | ENSG00000162769 | 0.01 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.07 | 0.07 | 0.06 | 0.01 | 0.00 | 0.05 | 0.04 | 0.09 | 0.02 | 0.09 | 0.01 | 0.05 | 0.00 | 0.17 | 0.04 | 0.05 | 0.02 | 0.04 | 0.01 | 0.07 | 0.03 | 0.00 | 0.01 | 0.15 | 0.01 | 0.16 | 0.02 | 0.01 | 0.04 | 0.00 | 0.01 | 0.00 | 0.00 | 0.20 | 0.02 | 0.16 | 0.17 | 0.06 | 0.01 | 0.05 | 0.02 | 0.11 | 0.04 | 0.06 | 0.21 | 0.02 | 0.03 | 0.01 | 0.00 | 0.16 | 0.04 | 0.00 | 0.02 | 0.01 | 0.06 | 0.09 | 0.00 | 0.11 | 0.03 |
| OXER1 | ENSG00000162881 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.07 | 0.05 | 0.01 | 0.00 | 0.00 | 0.02 | 0.05 | 0.06 | 0.01 | 0.14 | 0.02 | 0.03 | 0.01 | 0.04 | 0.03 | 0.03 | 0.02 | 0.00 | 0.04 | 0.00 | 0.03 | 0.01 | 0.02 | 0.05 | 0.01 | 0.05 | 0.05 | 0.05 | 0.03 | 0.00 | 0.01 | 0.00 | 0.00 | 0.06 | 0.02 | 0.26 | 0.05 | 0.08 | 0.00 | 0.06 | 0.02 | 0.24 | 0.00 | 0.05 | 0.06 | 0.17 | 0.01 | 0.00 | 0.00 | 0.10 | 0.02 | 0.01 | 0.00 | 0.01 | 0.01 | 0.03 | 0.00 | 0.01 | 0.01 |
| IL20 | ENSG00000162891 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.02 | 0.07 | 0.06 | 0.01 | 0.00 | 0.07 | 0.01 | 0.12 | 0.01 | 0.10 | 0.01 | 0.05 | 0.00 | 0.18 | 0.06 | 0.11 | 0.01 | 0.04 | 0.00 | 0.12 | 0.02 | 0.00 | 0.00 | 0.19 | 0.01 | 0.18 | 0.02 | 0.01 | 0.03 | 0.01 | 0.00 | 0.00 | 0.00 | 0.28 | 0.01 | 0.22 | 0.11 | 0.07 | 0.00 | 0.07 | 0.02 | 0.20 | 0.04 | 0.04 | 0.18 | 0.03 | 0.02 | 0.01 | 0.00 | 0.16 | 0.10 | 0.00 | 0.01 | 0.04 | 0.02 | 0.09 | 0.00 | 0.15 | 0.02 |
| IL24 | ENSG00000162892 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.02 | 0.07 | 0.06 | 0.01 | 0.00 | 0.07 | 0.01 | 0.12 | 0.01 | 0.10 | 0.01 | 0.05 | 0.00 | 0.18 | 0.06 | 0.12 | 0.01 | 0.04 | 0.00 | 0.12 | 0.02 | 0.00 | 0.00 | 0.20 | 0.01 | 0.18 | 0.02 | 0.01 | 0.03 | 0.01 | 0.00 | 0.00 | 0.00 | 0.28 | 0.01 | 0.22 | 0.11 | 0.07 | 0.00 | 0.07 | 0.02 | 0.20 | 0.04 | 0.04 | 0.18 | 0.03 | 0.02 | 0.01 | 0.00 | 0.16 | 0.10 | 0.00 | 0.01 | 0.04 | 0.02 | 0.09 | 0.00 | 0.15 | 0.02 |
| PIGR | ENSG00000162896 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.02 | 0.07 | 0.06 | 0.01 | 0.00 | 0.07 | 0.01 | 0.12 | 0.01 | 0.10 | 0.01 | 0.05 | 0.00 | 0.18 | 0.06 | 0.12 | 0.01 | 0.04 | 0.00 | 0.12 | 0.02 | 0.00 | 0.00 | 0.19 | 0.01 | 0.18 | 0.02 | 0.01 | 0.03 | 0.01 | 0.00 | 0.00 | 0.00 | 0.28 | 0.01 | 0.22 | 0.11 | 0.07 | 0.00 | 0.07 | 0.02 | 0.20 | 0.04 | 0.04 | 0.18 | 0.03 | 0.02 | 0.01 | 0.00 | 0.16 | 0.10 | 0.00 | 0.01 | 0.04 | 0.02 | 0.09 | 0.00 | 0.15 | 0.02 |
| KCNF1 | ENSG00000162975 | 0.00 | 0.00 | 0.01 | 0.02 | 0.00 | 0.06 | 0.02 | 0.01 | 0.11 | 0.02 | 0.00 | 0.00 | 0.03 | 0.03 | 0.04 | 0.02 | 0.09 | 0.05 | 0.02 | 0.04 | 0.04 | 0.06 | 0.05 | 0.04 | 0.01 | 0.01 | 0.02 | 0.03 | 0.01 | 0.03 | 0.13 | 0.01 | 0.00 | 0.05 | 0.01 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.07 | 0.06 | 0.23 | 0.17 | 0.08 | 0.01 | 0.09 | 0.03 | 0.28 | 0.07 | 0.05 | 0.11 | 0.16 | 0.01 | 0.00 | 0.00 | 0.03 | 0.08 | 0.02 | 0.01 | 0.04 | 0.02 | 0.05 | 0.00 | 0.01 | 0.04 |
| FRZB | ENSG00000162998 | 0.02 | 0.01 | 0.07 | 0.00 | 0.00 | 0.00 | 0.01 | 0.07 | 0.06 | 0.05 | 0.00 | 0.00 | 0.00 | 0.03 | 0.07 | 0.01 | 0.16 | 0.03 | 0.15 | 0.01 | 0.14 | 0.03 | 0.06 | 0.05 | 0.01 | 0.01 | 0.02 | 0.02 | 0.03 | 0.01 | 0.04 | 0.03 | 0.00 | 0.05 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.02 | 0.36 | 0.05 | 0.12 | 0.03 | 0.06 | 0.01 | 0.13 | 0.00 | 0.03 | 0.07 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.03 | 0.02 |
| DUSP19 | ENSG00000162999 | 0.02 | 0.01 | 0.07 | 0.00 | 0.00 | 0.00 | 0.01 | 0.07 | 0.06 | 0.05 | 0.00 | 0.00 | 0.00 | 0.01 | 0.06 | 0.01 | 0.16 | 0.03 | 0.15 | 0.01 | 0.15 | 0.03 | 0.06 | 0.05 | 0.01 | 0.01 | 0.02 | 0.02 | 0.03 | 0.01 | 0.05 | 0.03 | 0.00 | 0.05 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.02 | 0.35 | 0.05 | 0.12 | 0.02 | 0.07 | 0.01 | 0.03 | 0.00 | 0.03 | 0.07 | 0.04 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.03 | 0.01 |
| H3F3A | ENSG00000163041 | 0.01 | 0.02 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.08 | 0.10 | 0.04 | 0.02 | 0.02 | 0.05 | 0.01 | 0.08 | 0.01 | 0.13 | 0.02 | 0.06 | 0.00 | 0.21 | 0.04 | 0.14 | 0.01 | 0.03 | 0.01 | 0.05 | 0.01 | 0.01 | 0.01 | 0.13 | 0.03 | 0.18 | 0.02 | 0.04 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.23 | 0.02 | 0.40 | 0.05 | 0.07 | 0.01 | 0.10 | 0.02 | 0.26 | 0.00 | 0.04 | 0.24 | 0.03 | 0.05 | 0.02 | 0.00 | 0.02 | 0.15 | 0.00 | 0.02 | 0.02 | 0.05 | 0.09 | 0.00 | 0.13 | 0.05 |
| INHBB | ENSG00000163083 | 0.00 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.13 | 0.06 | 0.01 | 0.00 | 0.01 | 0.02 | 0.00 | 0.06 | 0.01 | 0.14 | 0.01 | 0.12 | 0.01 | 0.31 | 0.03 | 0.06 | 0.03 | 0.00 | 0.01 | 0.01 | 0.00 | 0.01 | 0.01 | 0.01 | 0.04 | 0.00 | 0.01 | 0.05 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.04 | 0.10 | 0.13 | 0.03 | 0.01 | 0.05 | 0.01 | 0.22 | 0.00 | 0.15 | 0.02 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.08 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 |
| BIRC8 | ENSG00000163098 | 0.01 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.02 | 0.00 | 0.19 | 0.03 | 0.00 | 0.00 | 0.01 | 0.06 | 0.02 | 0.06 | 0.07 | 0.09 | 0.03 | 0.02 | 0.08 | 0.03 | 0.09 | 0.03 | 0.02 | 0.03 | 0.01 | 0.04 | 0.03 | 0.04 | 0.06 | 0.03 | 0.00 | 0.07 | 0.22 | 0.00 | 0.00 | 0.03 | 0.00 | 0.00 | 0.14 | 0.03 | 0.12 | 0.28 | 0.10 | 0.05 | 0.05 | 0.05 | 0.45 | 0.10 | 0.07 | 0.17 | 0.00 | 0.06 | 0.01 | 0.00 | 0.13 | 0.03 | 0.01 | 0.17 | 0.02 | 0.14 | 0.00 | 0.00 | 0.04 | 0.03 |
| HPGDS | ENSG00000163106 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.03 | 0.05 | 0.05 | 0.00 | 0.00 | 0.00 | 0.05 | 0.01 | 0.03 | 0.04 | 0.05 | 0.04 | 0.03 | 0.02 | 0.09 | 0.02 | 0.07 | 0.01 | 0.01 | 0.00 | 0.02 | 0.00 | 0.01 | 0.01 | 0.09 | 0.00 | 0.06 | 0.04 | 0.02 | 0.02 | 0.02 | 0.00 | 0.00 | 0.04 | 0.04 | 0.05 | 0.27 | 0.01 | 0.03 | 0.02 | 0.04 | 0.03 | 0.11 | 0.05 | 0.09 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.02 | 0.01 | 0.01 | 0.00 | 0.00 | 0.03 | 0.04 |
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