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 |
| TIMP3 | ENSG00000100234 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.02 | 0.15 | 0.02 | 0.02 | 0.03 | 0.00 | 0.01 | 0.04 | 0.03 | 0.10 | 0.01 | 0.01 | 0.00 | 0.04 | 0.02 | 0.02 | 0.02 | 0.02 | 0.01 | 0.02 | 0.01 | 0.00 | 0.01 | 0.04 | 0.01 | 0.00 | 0.01 | 0.00 | 0.02 | 0.00 | 0.02 | 0.00 | 0.00 | 0.02 | 0.03 | 0.15 | 0.07 | 0.03 | 0.01 | 0.05 | 0.02 | 0.12 | 0.10 | 0.11 | 0.05 | 0.04 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.00 | 0.04 | 0.01 | 0.00 | 0.06 | 0.04 |
| LTBR | ENSG00000111321 | 0.01 | 0.00 | 0.00 | 0.01 | 0.02 | 0.00 | 0.01 | 0.07 | 0.10 | 0.02 | 0.01 | 0.00 | 0.00 | 0.08 | 0.07 | 0.07 | 0.17 | 0.02 | 0.11 | 0.02 | 0.10 | 0.05 | 0.06 | 0.05 | 0.06 | 0.02 | 0.05 | 0.02 | 0.05 | 0.05 | 0.04 | 0.04 | 0.14 | 0.05 | 0.05 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.13 | 0.04 | 0.37 | 0.08 | 0.05 | 0.02 | 0.10 | 0.02 | 0.15 | 0.03 | 0.08 | 0.12 | 0.58 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.16 | 0.01 | 0.05 | 0.02 | 0.00 | 0.01 | 0.05 | 0.04 |
| PRKAR2B | ENSG00000005249 | 0.01 | 0.00 | 0.05 | 0.01 | 0.01 | 0.00 | 0.05 | 0.03 | 0.05 | 0.02 | 0.00 | 0.00 | 0.03 | 0.00 | 0.10 | 0.03 | 0.14 | 0.03 | 0.16 | 0.02 | 0.35 | 0.07 | 0.14 | 0.04 | 0.01 | 0.00 | 0.01 | 0.00 | 0.04 | 0.02 | 0.07 | 0.02 | 0.00 | 0.02 | 0.02 | 0.06 | 0.00 | 0.02 | 0.00 | 0.00 | 0.06 | 0.04 | 0.25 | 0.06 | 0.04 | 0.03 | 0.02 | 0.03 | 0.12 | 0.05 | 0.14 | 0.02 | 0.08 | 0.01 | 0.00 | 0.02 | 0.13 | 0.00 | 0.09 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.08 | 0.03 |
| IL20RA | ENSG00000016402 | 0.00 | 0.05 | 0.00 | 0.01 | 0.00 | 0.05 | 0.01 | 0.01 | 0.08 | 0.05 | 0.00 | 0.01 | 0.00 | 0.14 | 0.03 | 0.04 | 0.05 | 0.03 | 0.07 | 0.02 | 0.13 | 0.01 | 0.11 | 0.02 | 0.02 | 0.00 | 0.04 | 0.00 | 0.03 | 0.02 | 0.01 | 0.08 | 0.00 | 0.10 | 0.16 | 0.02 | 0.00 | 0.02 | 0.00 | 0.00 | 0.10 | 0.06 | 0.07 | 0.28 | 0.03 | 0.04 | 0.05 | 0.02 | 0.08 | 0.03 | 0.39 | 0.03 | 0.01 | 0.04 | 0.00 | 0.00 | 0.00 | 0.25 | 0.00 | 0.05 | 0.01 | 0.11 | 0.06 | 0.09 | 0.02 | 0.14 |
| ADAMTSL3 | ENSG00000156218 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.02 | 0.02 | 0.02 | 0.04 | 0.02 | 0.03 | 0.00 | 0.11 | 0.00 | 0.03 | 0.01 | 0.14 | 0.01 | 0.04 | 0.02 | 0.11 | 0.03 | 0.11 | 0.02 | 0.04 | 0.01 | 0.03 | 0.00 | 0.05 | 0.01 | 0.07 | 0.03 | 0.05 | 0.01 | 0.06 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.13 | 0.02 | 0.25 | 0.09 | 0.16 | 0.01 | 0.03 | 0.03 | 0.19 | 0.06 | 0.10 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.00 | 0.01 | 0.01 | 0.01 | 0.02 | 0.00 | 0.00 | 0.16 | 0.01 |
| MTM1 | ENSG00000171100 | 0.03 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.03 | 0.01 | 0.10 | 0.04 | 0.06 | 0.00 | 0.06 | 0.01 | 0.21 | 0.01 | 0.17 | 0.02 | 0.12 | 0.00 | 0.17 | 0.04 | 0.17 | 0.02 | 0.04 | 0.01 | 0.08 | 0.04 | 0.06 | 0.00 | 0.10 | 0.02 | 0.10 | 0.01 | 0.07 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.10 | 0.02 | 0.39 | 0.10 | 0.21 | 0.02 | 0.08 | 0.02 | 0.13 | 0.07 | 0.15 | 0.12 | 0.00 | 0.02 | 0.00 | 0.00 | 0.15 | 0.04 | 0.03 | 0.03 | 0.02 | 0.02 | 0.05 | 0.00 | 0.07 | 0.01 |
| SLC30A10 | ENSG00000196660 | 0.02 | 0.02 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.06 | 0.09 | 0.06 | 0.02 | 0.02 | 0.07 | 0.01 | 0.08 | 0.01 | 0.12 | 0.01 | 0.05 | 0.00 | 0.22 | 0.03 | 0.06 | 0.01 | 0.02 | 0.00 | 0.08 | 0.02 | 0.00 | 0.01 | 0.14 | 0.02 | 0.16 | 0.02 | 0.08 | 0.02 | 0.00 | 0.01 | 0.01 | 0.00 | 0.22 | 0.02 | 0.29 | 0.12 | 0.07 | 0.01 | 0.07 | 0.02 | 0.16 | 0.00 | 0.04 | 0.21 | 0.02 | 0.03 | 0.01 | 0.00 | 0.11 | 0.07 | 0.00 | 0.02 | 0.01 | 0.06 | 0.14 | 0.00 | 0.12 | 0.03 |
| BMP5 | ENSG00000112175 | 0.00 | 0.00 | 0.03 | 0.02 | 0.00 | 0.00 | 0.00 | 0.01 | 0.09 | 0.04 | 0.00 | 0.00 | 0.01 | 0.00 | 0.07 | 0.02 | 0.26 | 0.03 | 0.12 | 0.02 | 0.23 | 0.03 | 0.11 | 0.02 | 0.02 | 0.01 | 0.08 | 0.01 | 0.03 | 0.00 | 0.07 | 0.00 | 0.03 | 0.00 | 0.03 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.09 | 0.03 | 0.16 | 0.05 | 0.09 | 0.04 | 0.05 | 0.01 | 0.23 | 0.03 | 0.12 | 0.05 | 0.04 | 0.00 | 0.00 | 0.00 | 0.09 | 0.00 | 0.01 | 0.00 | 0.01 | 0.02 | 0.05 | 0.00 | 0.07 | 0.02 |
| MBOAT1 | ENSG00000172197 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.02 | 1.12 | 0.01 | 0.00 | 0.01 | 0.01 | 0.03 | 0.06 | 0.01 | 0.14 | 0.06 | 0.04 | 0.05 | 0.19 | 0.15 | 0.08 | 0.06 | 0.02 | 0.04 | 0.01 | 0.03 | 0.02 | 0.06 | 0.15 | 0.02 | 0.06 | 0.03 | 0.04 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.18 | 0.02 | 0.53 | 0.03 | 0.11 | 0.05 | 0.07 | 0.02 | 0.29 | 0.02 | 0.06 | 0.11 | 0.02 | 0.02 | 0.00 | 0.00 | 0.05 | 0.00 | 0.01 | 0.01 | 0.04 | 0.01 | 0.21 | 0.00 | 0.19 | 0.00 |
| AGTR1 | ENSG00000144891 | 0.03 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.05 | 0.02 | 0.11 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 | 0.09 | 0.01 | 0.76 | 0.01 | 0.42 | 0.00 | 0.47 | 0.01 | 0.09 | 0.01 | 0.01 | 0.00 | 0.05 | 0.01 | 0.02 | 0.00 | 0.08 | 0.01 | 0.03 | 0.03 | 0.09 | 0.01 | 0.00 | 0.05 | 0.00 | 0.00 | 0.13 | 0.01 | 0.64 | 0.02 | 0.38 | 0.01 | 0.13 | 0.01 | 0.30 | 0.02 | 0.07 | 0.07 | 0.07 | 0.00 | 0.00 | 0.00 | 0.01 | 0.05 | 0.00 | 0.01 | 0.02 | 0.03 | 0.00 | 0.00 | 0.04 | 0.04 |
| ATP2B2 | ENSG00000157087 | 0.00 | 0.18 | 0.00 | 0.01 | 0.07 | 0.00 | 0.01 | 0.06 | 0.43 | 0.03 | 0.00 | 0.03 | 0.03 | 0.06 | 0.04 | 0.04 | 0.03 | 0.04 | 0.01 | 0.02 | 0.08 | 0.06 | 0.06 | 0.05 | 0.00 | 0.04 | 0.03 | 0.06 | 0.01 | 0.02 | 0.09 | 0.01 | 0.00 | 0.18 | 0.07 | 0.01 | 0.00 | 0.04 | 0.00 | 0.00 | 0.12 | 0.03 | 0.15 | 0.22 | 0.02 | 0.02 | 0.05 | 0.03 | 0.05 | 0.17 | 0.26 | 0.05 | 0.04 | 0.05 | 0.00 | 0.00 | 0.00 | 0.05 | 0.03 | 0.01 | 0.03 | 0.02 | 0.00 | 0.00 | 0.02 | 0.05 |
| METAP1D | ENSG00000172878 | 0.02 | 0.00 | 0.08 | 0.00 | 0.00 | 0.00 | 0.01 | 0.09 | 0.07 | 0.04 | 0.00 | 0.01 | 0.00 | 0.00 | 0.05 | 0.01 | 0.13 | 0.02 | 0.13 | 0.01 | 0.25 | 0.01 | 0.04 | 0.03 | 0.01 | 0.01 | 0.03 | 0.02 | 0.03 | 0.02 | 0.06 | 0.06 | 0.05 | 0.01 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.03 | 0.37 | 0.03 | 0.09 | 0.01 | 0.08 | 0.01 | 0.16 | 0.00 | 0.03 | 0.10 | 0.04 | 0.01 | 0.00 | 0.00 | 0.00 | 0.06 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.02 |
| VCL | ENSG00000035403 | 0.00 | 0.01 | 0.00 | 0.00 | 0.03 | 0.00 | 0.01 | 0.06 | 0.13 | 0.03 | 0.00 | 0.00 | 0.01 | 0.00 | 0.03 | 0.02 | 0.07 | 0.05 | 0.04 | 0.04 | 0.07 | 0.04 | 0.18 | 0.05 | 0.03 | 0.03 | 0.10 | 0.04 | 0.02 | 0.00 | 0.05 | 0.03 | 0.25 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.13 | 0.03 | 0.23 | 0.11 | 0.01 | 0.01 | 0.15 | 0.04 | 0.23 | 0.02 | 0.06 | 0.11 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.00 | 0.01 | 0.02 |
| PRPS1 | ENSG00000147224 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.05 | 0.03 | 0.03 | 0.00 | 0.00 | 0.04 | 0.03 | 0.01 | 0.13 | 0.01 | 0.03 | 0.01 | 0.10 | 0.02 | 0.07 | 0.01 | 0.02 | 0.01 | 0.02 | 0.01 | 0.00 | 0.01 | 0.02 | 0.01 | 0.00 | 0.01 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.02 | 0.10 | 0.06 | 0.03 | 0.00 | 0.03 | 0.02 | 0.03 | 0.02 | 0.08 | 0.10 | 0.00 | 0.01 | 0.00 | 0.00 | 0.04 | 0.02 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 |
| FSTL4 | ENSG00000053108 | 0.28 | 0.01 | 0.03 | 0.01 | 0.00 | 0.00 | 0.03 | 0.05 | 0.04 | 0.04 | 0.00 | 0.00 | 0.00 | 0.05 | 0.00 | 0.08 | 0.00 | 0.06 | 0.01 | 0.05 | 0.03 | 0.06 | 0.01 | 0.11 | 0.01 | 0.05 | 0.02 | 0.04 | 0.01 | 0.04 | 0.07 | 0.04 | 0.09 | 0.01 | 0.32 | 0.02 | 0.00 | 0.04 | 0.01 | 0.00 | 0.03 | 0.05 | 0.13 | 0.18 | 0.03 | 0.03 | 0.01 | 0.02 | 0.15 | 0.04 | 0.04 | 0.06 | 0.01 | 0.00 | 0.00 | 0.10 | 0.04 | 0.00 | 0.01 | 0.04 | 0.01 | 0.02 | 0.00 | 0.03 | 0.01 | 0.10 |
| PLBD1 | ENSG00000121316 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.11 | 0.02 | 0.06 | 0.01 | 0.00 | 0.00 | 0.06 | 0.03 | 0.10 | 0.08 | 0.02 | 0.05 | 0.03 | 0.13 | 0.04 | 0.03 | 0.07 | 0.01 | 0.03 | 0.00 | 0.06 | 0.01 | 0.07 | 0.01 | 0.05 | 0.14 | 0.05 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.06 | 0.07 | 0.24 | 0.13 | 0.01 | 0.03 | 0.03 | 0.02 | 0.09 | 0.03 | 0.13 | 0.14 | 0.56 | 0.00 | 0.00 | 0.04 | 0.00 | 0.04 | 0.03 | 0.02 | 0.00 | 0.06 | 0.00 | 0.01 | 0.04 | 0.02 |
| PCK1 | ENSG00000124253 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.00 | 0.06 | 0.03 | 0.00 | 0.00 | 0.03 | 0.00 | 0.23 | 0.02 | 0.05 | 0.03 | 0.01 | 0.01 | 0.11 | 0.01 | 0.22 | 0.00 | 0.14 | 0.00 | 0.09 | 0.00 | 0.03 | 0.00 | 0.12 | 0.00 | 0.00 | 0.01 | 0.04 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.38 | 0.02 | 0.41 | 0.04 | 0.03 | 0.02 | 0.09 | 0.01 | 0.21 | 0.00 | 0.21 | 0.04 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.03 | 0.02 | 0.00 | 0.00 | 0.11 | 0.01 |
| PPT1 | ENSG00000131238 | 0.01 | 0.02 | 0.01 | 0.04 | 0.00 | 0.00 | 0.01 | 0.01 | 0.31 | 0.02 | 0.00 | 0.00 | 0.11 | 0.03 | 0.13 | 0.02 | 0.16 | 0.02 | 0.09 | 0.02 | 0.34 | 0.02 | 0.07 | 0.03 | 0.05 | 0.02 | 0.01 | 0.03 | 0.04 | 0.01 | 0.03 | 0.10 | 0.00 | 0.26 | 0.00 | 0.03 | 0.03 | 0.07 | 0.00 | 0.00 | 0.09 | 0.05 | 0.74 | 0.05 | 0.07 | 0.01 | 0.14 | 0.01 | 0.22 | 0.05 | 0.11 | 0.03 | 0.04 | 0.03 | 0.02 | 0.00 | 0.00 | 0.03 | 0.00 | 0.01 | 0.03 | 0.02 | 0.00 | 0.10 | 0.05 | 0.03 |
| FCGR2A | ENSG00000143226 | 0.03 | 0.00 | 0.01 | 0.01 | 0.00 | 0.03 | 0.02 | 0.04 | 0.83 | 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 | 0.30 | 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 | 0.17 | 0.00 | 0.13 | 0.00 | 0.28 | 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 |
| SFMBT1 | ENSG00000163935 | 0.00 | 0.16 | 0.00 | 0.02 | 0.00 | 0.02 | 0.00 | 0.03 | 0.03 | 0.16 | 0.00 | 0.03 | 0.00 | 0.57 | 0.01 | 0.06 | 0.00 | 0.11 | 0.00 | 0.06 | 0.06 | 0.15 | 0.01 | 0.11 | 0.00 | 0.06 | 0.02 | 0.07 | 0.00 | 0.04 | 0.04 | 0.07 | 0.00 | 0.20 | 0.16 | 0.01 | 0.00 | 0.04 | 0.00 | 0.00 | 0.01 | 0.17 | 0.09 | 0.21 | 0.00 | 0.07 | 0.05 | 0.08 | 0.00 | 0.32 | 0.03 | 0.15 | 0.05 | 0.01 | 0.00 | 0.01 | 0.00 | 0.06 | 0.01 | 0.06 | 0.00 | 0.04 | 0.00 | 0.03 | 0.02 | 0.04 |
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