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 |
| SLC10A7 | ENSG00000120519 | 0.01 | 0.02 | 0.00 | 0.01 | 0.06 | 0.00 | 0.01 | 0.02 | 0.12 | 0.08 | 0.00 | 0.00 | 0.00 | 0.01 | 0.03 | 0.04 | 0.02 | 0.11 | 0.03 | 0.04 | 0.15 | 0.03 | 0.08 | 0.05 | 0.01 | 0.02 | 0.02 | 0.02 | 0.00 | 0.02 | 0.05 | 0.06 | 0.00 | 0.08 | 0.10 | 0.05 | 0.00 | 0.02 | 0.00 | 0.00 | 0.06 | 0.05 | 0.11 | 0.17 | 0.03 | 0.07 | 0.04 | 0.03 | 0.09 | 0.04 | 0.16 | 0.08 | 0.00 | 0.01 | 0.00 | 0.00 | 0.03 | 0.03 | 0.01 | 0.08 | 0.00 | 0.03 | 0.00 | 0.00 | 0.04 | 0.04 |
| BMP6 | ENSG00000153162 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.06 | 0.27 | 0.06 | 0.00 | 0.06 | 0.03 | 0.02 | 0.11 | 0.01 | 0.09 | 0.08 | 0.06 | 0.06 | 0.08 | 0.22 | 0.05 | 0.10 | 0.02 | 0.03 | 0.02 | 0.04 | 0.00 | 0.07 | 0.15 | 0.02 | 0.06 | 0.06 | 0.06 | 0.07 | 0.00 | 0.01 | 0.00 | 0.00 | 0.14 | 0.06 | 0.48 | 0.09 | 0.08 | 0.06 | 0.07 | 0.02 | 0.19 | 0.05 | 0.08 | 0.14 | 0.04 | 0.03 | 0.00 | 0.00 | 0.10 | 0.01 | 0.02 | 0.03 | 0.01 | 0.03 | 0.25 | 0.00 | 0.24 | 0.01 |
| SLC34A2 | ENSG00000157765 | 0.01 | 0.00 | 0.00 | 0.00 | 0.04 | 0.00 | 0.00 | 0.05 | 0.02 | 0.03 | 0.00 | 0.00 | 0.00 | 0.03 | 0.06 | 0.02 | 0.03 | 0.06 | 0.07 | 0.04 | 0.05 | 0.04 | 0.01 | 0.02 | 0.01 | 0.02 | 0.03 | 0.01 | 0.00 | 0.01 | 0.02 | 0.03 | 0.00 | 0.01 | 0.05 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.04 | 0.13 | 0.08 | 0.01 | 0.02 | 0.01 | 0.04 | 0.06 | 0.07 | 0.13 | 0.03 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.01 | 0.00 | 0.05 | 0.00 | 0.04 | 0.01 |
| ITGA11 | ENSG00000137809 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.02 | 0.04 | 0.01 | 0.00 | 0.00 | 0.09 | 0.00 | 0.03 | 0.03 | 0.05 | 0.02 | 0.02 | 0.02 | 0.05 | 0.04 | 0.04 | 0.02 | 0.01 | 0.01 | 0.01 | 0.03 | 0.03 | 0.02 | 0.02 | 0.02 | 0.00 | 0.01 | 0.04 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.04 | 0.15 | 0.11 | 0.07 | 0.02 | 0.01 | 0.04 | 0.07 | 0.12 | 0.13 | 0.05 | 0.01 | 0.01 | 0.00 | 0.00 | 0.06 | 0.00 | 0.01 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.10 | 0.00 |
| MMRN1 | ENSG00000138722 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.05 | 0.03 | 0.12 | 0.05 | 0.00 | 0.00 | 0.00 | 0.09 | 0.03 | 0.03 | 0.06 | 0.04 | 0.04 | 0.03 | 0.08 | 0.09 | 0.03 | 0.06 | 0.01 | 0.02 | 0.01 | 0.01 | 0.00 | 0.01 | 0.02 | 0.10 | 0.00 | 0.03 | 0.04 | 0.02 | 0.03 | 0.07 | 0.00 | 0.00 | 0.04 | 0.04 | 0.05 | 0.24 | 0.01 | 0.03 | 0.05 | 0.03 | 0.07 | 0.09 | 0.06 | 0.08 | 0.00 | 0.01 | 0.00 | 0.00 | 0.03 | 0.05 | 0.00 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.04 |
| CADM3 | ENSG00000162706 | 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 | 0.25 | 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 |
| DNMT3B | ENSG00000088305 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.02 | 0.01 | 0.25 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.07 | 0.01 | 0.20 | 0.00 | 0.18 | 0.00 | 0.08 | 0.00 | 0.05 | 0.01 | 0.11 | 0.00 | 0.18 | 0.00 | 0.01 | 0.01 | 0.02 | 0.00 | 0.00 | 0.01 | 0.05 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.07 | 0.02 | 0.23 | 0.02 | 0.19 | 0.00 | 0.09 | 0.01 | 0.48 | 0.00 | 0.08 | 0.02 | 0.03 | 0.00 | 0.01 | 0.02 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.01 |
| CCDC3 | ENSG00000151468 | 0.01 | 0.01 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.24 | 0.01 | 0.00 | 0.00 | 0.03 | 0.08 | 0.03 | 0.05 | 0.02 | 0.06 | 0.02 | 0.03 | 0.08 | 0.02 | 0.06 | 0.04 | 0.01 | 0.02 | 0.02 | 0.01 | 0.03 | 0.02 | 0.01 | 0.01 | 0.00 | 0.05 | 0.10 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.18 | 0.01 | 0.28 | 0.07 | 0.02 | 0.01 | 0.05 | 0.01 | 0.13 | 0.03 | 0.07 | 0.05 | 0.00 | 0.01 | 0.00 | 0.00 | 0.04 | 0.06 | 0.03 | 0.00 | 0.02 | 0.01 | 0.00 | 0.02 | 0.03 | 0.02 |
| STAT3 | ENSG00000168610 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.09 | 0.05 | 0.02 | 0.01 | 0.00 | 0.01 | 0.02 | 0.06 | 0.01 | 0.03 | 0.05 | 0.03 | 0.02 | 0.19 | 0.03 | 0.12 | 0.03 | 0.06 | 0.01 | 0.04 | 0.02 | 0.03 | 0.03 | 0.04 | 0.04 | 0.02 | 0.01 | 0.01 | 0.14 | 0.00 | 0.12 | 0.00 | 0.00 | 0.06 | 0.10 | 0.01 | 0.16 | 0.04 | 0.04 | 0.03 | 0.07 | 0.00 | 0.20 | 0.05 | 0.10 | 0.01 | 0.01 | 0.00 | 0.02 | 0.06 | 0.00 | 0.00 | 0.01 | 0.01 | 0.02 | 0.00 | 0.05 | 0.01 | 0.03 |
| KLHL32 | ENSG00000186231 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.32 | 0.01 | 0.11 | 0.00 | 0.00 | 0.02 | 0.08 | 0.01 | 0.05 | 0.03 | 0.05 | 0.02 | 0.03 | 0.01 | 0.12 | 0.03 | 0.07 | 0.00 | 0.03 | 0.01 | 0.02 | 0.00 | 0.03 | 0.01 | 0.06 | 0.00 | 0.08 | 0.06 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.07 | 0.10 | 0.14 | 0.16 | 0.01 | 0.01 | 0.02 | 0.01 | 0.03 | 0.05 | 0.12 | 0.12 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.26 | 0.00 | 0.01 | 0.00 | 0.04 | 0.05 | 0.03 | 0.03 | 0.06 |
| ADGRF5 | ENSG00000069122 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.02 | 0.02 | 0.11 | 0.03 | 0.00 | 0.00 | 0.01 | 0.02 | 0.13 | 0.02 | 0.17 | 0.04 | 0.07 | 0.02 | 0.27 | 0.03 | 0.19 | 0.01 | 0.05 | 0.00 | 0.12 | 0.01 | 0.02 | 0.00 | 0.08 | 0.00 | 0.00 | 0.08 | 0.06 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.10 | 0.03 | 0.23 | 0.07 | 0.06 | 0.03 | 0.06 | 0.01 | 0.03 | 0.03 | 0.15 | 0.03 | 0.02 | 0.01 | 0.00 | 0.00 | 0.09 | 0.02 | 0.01 | 0.00 | 0.01 | 0.02 | 0.02 | 0.00 | 0.06 | 0.01 |
| ST14 | ENSG00000149418 | 0.00 | 0.01 | 0.00 | 0.04 | 0.00 | 0.05 | 0.03 | 0.04 | 0.03 | 0.11 | 0.00 | 0.00 | 0.14 | 0.06 | 0.06 | 0.09 | 0.04 | 0.13 | 0.04 | 0.15 | 0.09 | 0.15 | 0.06 | 0.07 | 0.02 | 0.01 | 0.01 | 0.02 | 0.02 | 0.02 | 0.03 | 0.09 | 0.00 | 0.23 | 0.02 | 0.06 | 0.00 | 0.05 | 0.00 | 0.00 | 0.05 | 0.21 | 0.28 | 0.19 | 0.04 | 0.31 | 0.06 | 0.07 | 0.18 | 0.19 | 0.04 | 0.23 | 0.00 | 0.28 | 0.04 | 0.00 | 0.13 | 0.00 | 0.05 | 0.01 | 0.01 | 0.01 | 0.00 | 0.07 | 0.01 | 0.26 |
| SLC12A8 | ENSG00000221955 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.04 | 0.05 | 0.02 | 0.01 | 0.01 | 0.00 | 0.01 | 0.04 | 0.02 | 0.12 | 0.01 | 0.04 | 0.00 | 0.10 | 0.07 | 0.07 | 0.02 | 0.00 | 0.01 | 0.03 | 0.01 | 0.00 | 0.00 | 0.03 | 0.02 | 0.00 | 0.05 | 0.04 | 0.01 | 0.00 | 0.05 | 0.00 | 0.00 | 0.03 | 0.04 | 0.29 | 0.04 | 0.08 | 0.01 | 0.07 | 0.01 | 0.13 | 0.08 | 0.10 | 0.06 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.03 | 0.02 | 0.06 | 0.00 | 0.00 | 0.00 | 0.04 |
| PTH2R | ENSG00000144407 | 0.02 | 0.04 | 0.05 | 0.03 | 0.00 | 0.03 | 0.02 | 0.02 | 0.02 | 0.20 | 0.00 | 0.00 | 0.00 | 0.15 | 0.05 | 0.02 | 0.06 | 0.14 | 0.03 | 0.16 | 0.09 | 0.10 | 0.09 | 0.03 | 0.03 | 0.01 | 0.03 | 0.01 | 0.09 | 0.01 | 0.04 | 0.03 | 0.00 | 0.05 | 0.03 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.06 | 0.04 | 0.21 | 0.13 | 0.03 | 0.30 | 0.04 | 0.03 | 0.06 | 0.05 | 0.05 | 0.15 | 0.06 | 0.01 | 0.00 | 0.02 | 0.00 | 0.04 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.02 | 0.02 | 0.03 |
| FKBP10 | ENSG00000141756 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.06 | 0.02 | 0.00 | 0.00 | 0.01 | 0.02 | 0.05 | 0.01 | 0.04 | 0.05 | 0.02 | 0.01 | 0.78 | 0.02 | 0.51 | 0.02 | 0.06 | 0.00 | 0.03 | 0.02 | 0.05 | 0.03 | 0.02 | 0.03 | 0.02 | 0.01 | 0.01 | 0.16 | 0.00 | 0.11 | 0.00 | 0.00 | 0.09 | 0.09 | 0.04 | 0.14 | 0.04 | 0.05 | 0.05 | 0.06 | 0.19 | 0.08 | 0.04 | 0.12 | 0.01 | 0.01 | 0.00 | 0.02 | 0.04 | 0.00 | 0.00 | 0.01 | 0.01 | 0.03 | 0.00 | 0.05 | 0.01 | 0.03 |
| NR5A1 | ENSG00000136931 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.02 | 0.03 | 0.00 | 0.01 | 0.00 | 0.02 | 0.04 | 0.02 | 0.05 | 0.03 | 0.06 | 0.01 | 0.10 | 0.02 | 0.08 | 0.01 | 0.02 | 0.01 | 0.05 | 0.02 | 0.00 | 0.01 | 0.03 | 0.03 | 0.06 | 0.04 | 0.10 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.07 | 0.03 | 0.10 | 0.15 | 0.05 | 0.01 | 0.01 | 0.04 | 0.10 | 0.16 | 0.12 | 0.04 | 0.01 | 0.02 | 0.01 | 0.00 | 0.05 | 0.00 | 0.01 | 0.00 | 0.04 | 0.02 | 0.00 | 0.00 | 0.02 | 0.03 |
| C1QTNF6 | ENSG00000133466 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.11 | 0.05 | 0.00 | 0.04 | 0.00 | 0.07 | 0.06 | 0.04 | 0.07 | 0.02 | 0.01 | 0.01 | 0.03 | 0.02 | 0.02 | 0.02 | 0.01 | 0.01 | 0.02 | 0.01 | 0.03 | 0.01 | 0.06 | 0.01 | 0.00 | 0.01 | 0.02 | 0.02 | 0.00 | 0.04 | 0.00 | 0.00 | 0.03 | 0.02 | 0.10 | 0.11 | 0.03 | 0.01 | 0.05 | 0.02 | 0.30 | 0.06 | 0.04 | 0.02 | 0.02 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.00 | 0.03 | 0.00 | 0.00 | 0.13 | 0.02 |
| SMG1 | ENSG00000157106 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.11 | 0.06 | 0.00 | 0.00 | 0.01 | 0.02 | 0.02 | 0.02 | 0.04 | 0.03 | 0.02 | 0.02 | 0.07 | 0.03 | 0.05 | 0.02 | 0.02 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.05 | 0.01 | 0.00 | 0.05 | 0.02 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.05 | 0.02 | 0.16 | 0.07 | 0.06 | 0.00 | 0.07 | 0.01 | 0.17 | 0.00 | 0.04 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.00 | 0.00 | 0.01 | 0.00 | 0.02 | 0.03 | 0.00 | 0.03 | 0.01 |
| SPP1 | ENSG00000118785 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.03 | 0.03 | 0.12 | 0.05 | 0.00 | 0.00 | 0.00 | 0.06 | 0.02 | 0.03 | 0.06 | 0.04 | 0.04 | 0.02 | 0.04 | 0.07 | 0.03 | 0.06 | 0.01 | 0.02 | 0.00 | 0.01 | 0.00 | 0.01 | 0.02 | 0.11 | 0.00 | 0.03 | 0.04 | 0.02 | 0.02 | 0.02 | 0.00 | 0.00 | 0.04 | 0.04 | 0.04 | 0.23 | 0.01 | 0.03 | 0.02 | 0.02 | 0.02 | 0.09 | 0.05 | 0.07 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.05 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.05 |
| ITGA10 | ENSG00000143127 | 0.03 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.04 | 0.03 | 0.50 | 0.04 | 0.02 | 0.00 | 0.10 | 0.13 | 0.38 | 0.12 | 0.28 | 0.13 | 0.10 | 0.16 | 0.23 | 0.11 | 0.19 | 0.04 | 0.02 | 0.04 | 0.15 | 0.03 | 0.05 | 0.01 | 0.33 | 0.03 | 0.39 | 0.01 | 0.17 | 0.03 | 0.10 | 0.26 | 0.00 | 0.00 | 0.36 | 0.05 | 0.60 | 0.09 | 0.15 | 0.06 | 0.25 | 0.02 | 0.41 | 0.04 | 0.41 | 0.12 | 0.12 | 0.03 | 0.00 | 0.00 | 0.28 | 0.02 | 0.01 | 0.01 | 0.02 | 0.03 | 0.00 | 0.03 | 0.17 | 0.05 |
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