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 |
| C10orf54 | ENSG00000107738 | 0.00 | 0.01 | 0.00 | 0.01 | 0.03 | 0.00 | 0.01 | 0.04 | 0.04 | 0.03 | 0.00 | 0.00 | 0.01 | 0.00 | 0.03 | 0.02 | 0.07 | 0.04 | 0.04 | 0.02 | 0.05 | 0.02 | 0.15 | 0.02 | 0.03 | 0.03 | 0.09 | 0.05 | 0.01 | 0.02 | 0.03 | 0.03 | 0.25 | 0.06 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.11 | 0.03 | 0.17 | 0.12 | 0.01 | 0.01 | 0.08 | 0.03 | 0.11 | 0.03 | 0.02 | 0.12 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.04 | 0.00 | 0.00 | 0.00 | 0.02 |
| ABCC10 | ENSG00000124574 | 0.01 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 | 0.20 | 0.02 | 0.00 | 0.00 | 0.01 | 0.02 | 0.11 | 0.01 | 0.17 | 0.04 | 0.07 | 0.02 | 0.54 | 0.01 | 0.37 | 0.01 | 0.10 | 0.00 | 0.21 | 0.00 | 0.04 | 0.00 | 0.15 | 0.00 | 0.05 | 0.01 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.13 | 0.03 | 0.28 | 0.07 | 0.07 | 0.02 | 0.07 | 0.01 | 0.10 | 0.03 | 0.12 | 0.02 | 0.05 | 0.01 | 0.00 | 0.00 | 0.11 | 0.00 | 0.01 | 0.00 | 0.01 | 0.01 | 0.02 | 0.00 | 0.06 | 0.00 |
| ABHD16A | ENSG00000204427 | 0.01 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.00 | 0.15 | 0.04 | 0.00 | 0.00 | 0.02 | 0.02 | 0.08 | 0.02 | 0.06 | 0.05 | 0.03 | 0.04 | 0.13 | 0.05 | 0.12 | 0.04 | 0.03 | 0.02 | 0.07 | 0.02 | 0.05 | 0.01 | 0.11 | 0.01 | 0.05 | 0.03 | 0.08 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.09 | 0.03 | 0.29 | 0.06 | 0.17 | 0.01 | 0.05 | 0.01 | 0.10 | 0.03 | 0.06 | 0.07 | 0.01 | 0.01 | 0.00 | 0.00 | 0.02 | 0.17 | 0.01 | 0.01 | 0.00 | 0.01 | 0.11 | 0.00 | 0.12 | 0.01 |
| L3MBTL2 | ENSG00000100395 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.09 | 0.00 | 0.03 | 0.00 | 0.04 | 0.03 | 0.03 | 0.06 | 0.02 | 0.03 | 0.01 | 0.03 | 0.00 | 0.02 | 0.01 | 0.01 | 0.02 | 0.01 | 0.05 | 0.04 | 0.03 | 0.05 | 0.01 | 0.04 | 0.01 | 0.07 | 0.00 | 0.00 | 0.06 | 0.00 | 0.00 | 0.03 | 0.03 | 0.02 | 0.23 | 0.04 | 0.04 | 0.04 | 0.05 | 0.17 | 0.15 | 0.08 | 0.05 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.05 | 0.00 | 0.00 | 0.33 | 0.00 |
| MCOLN1 | ENSG00000090674 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.02 | 0.01 | 0.02 | 0.07 | 0.08 | 0.00 | 0.01 | 0.01 | 0.07 | 0.01 | 0.05 | 0.05 | 0.09 | 0.02 | 0.09 | 0.04 | 0.10 | 0.04 | 0.08 | 0.03 | 0.02 | 0.01 | 0.04 | 0.00 | 0.04 | 0.00 | 0.11 | 0.00 | 0.01 | 0.17 | 0.03 | 0.01 | 0.00 | 0.00 | 0.01 | 0.08 | 0.08 | 0.26 | 0.46 | 0.04 | 0.14 | 0.04 | 0.21 | 0.11 | 0.56 | 0.24 | 0.01 | 0.02 | 0.00 | 0.04 | 0.00 | 0.00 | 0.09 | 0.01 | 0.01 | 0.03 | 0.01 | 0.00 | 0.05 | 0.06 | 0.03 |
| MTMR1 | ENSG00000063601 | 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 | 0.20 | 0.01 | 0.18 | 0.02 | 0.11 | 0.00 | 0.17 | 0.01 | 0.16 | 0.02 | 0.04 | 0.00 | 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 | 0.10 | 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 |
| PRPSAP1 | ENSG00000161542 | 0.02 | 0.00 | 0.05 | 0.00 | 0.02 | 0.00 | 0.04 | 0.04 | 0.21 | 0.00 | 0.00 | 0.01 | 0.09 | 0.02 | 0.16 | 0.02 | 0.23 | 0.02 | 0.08 | 0.04 | 0.20 | 0.07 | 0.08 | 0.04 | 0.04 | 0.01 | 0.06 | 0.03 | 0.04 | 0.10 | 0.25 | 0.01 | 0.08 | 0.01 | 0.13 | 0.02 | 0.02 | 0.01 | 0.00 | 0.00 | 0.35 | 0.03 | 0.33 | 0.05 | 0.17 | 0.05 | 0.16 | 0.02 | 0.47 | 0.04 | 0.25 | 0.02 | 0.05 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.07 | 0.00 | 0.05 | 0.01 | 0.14 | 0.01 | 0.25 | 0.02 |
| ABCB11 | ENSG00000073734 | 0.02 | 0.00 | 0.04 | 0.01 | 0.00 | 0.00 | 0.01 | 0.09 | 0.08 | 0.04 | 0.00 | 0.01 | 0.00 | 0.00 | 0.05 | 0.01 | 0.09 | 0.02 | 0.08 | 0.01 | 0.11 | 0.02 | 0.06 | 0.04 | 0.01 | 0.01 | 0.01 | 0.02 | 0.02 | 0.01 | 0.05 | 0.06 | 0.00 | 0.01 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.03 | 0.30 | 0.05 | 0.08 | 0.01 | 0.04 | 0.01 | 0.06 | 0.00 | 0.05 | 0.08 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.07 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.02 |
| SULF2 | ENSG00000196562 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.01 | 0.11 | 0.01 | 0.00 | 0.00 | 0.02 | 0.00 | 0.09 | 0.04 | 0.07 | 0.03 | 0.01 | 0.01 | 0.05 | 0.00 | 0.21 | 0.01 | 0.13 | 0.00 | 0.12 | 0.00 | 0.00 | 0.00 | 0.05 | 0.01 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.19 | 0.02 | 0.34 | 0.02 | 0.01 | 0.04 | 0.12 | 0.01 | 0.40 | 0.00 | 0.12 | 0.04 | 0.01 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.06 | 0.00 |
| C1S | ENSG00000182326 | 0.01 | 0.00 | 0.00 | 0.01 | 0.02 | 0.00 | 0.01 | 0.07 | 0.09 | 0.02 | 0.01 | 0.00 | 0.00 | 0.08 | 0.07 | 0.07 | 0.18 | 0.01 | 0.11 | 0.02 | 0.07 | 0.02 | 0.06 | 0.05 | 0.06 | 0.02 | 0.04 | 0.03 | 0.06 | 0.05 | 0.05 | 0.04 | 0.18 | 0.05 | 0.09 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.13 | 0.04 | 0.35 | 0.08 | 0.04 | 0.02 | 0.09 | 0.02 | 0.17 | 0.03 | 0.08 | 0.11 | 0.60 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.14 | 0.01 | 0.06 | 0.02 | 0.00 | 0.01 | 0.04 | 0.04 |
| IVNS1ABP | ENSG00000116679 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.03 | 0.24 | 0.03 | 0.02 | 0.00 | 0.10 | 0.03 | 0.11 | 0.00 | 0.14 | 0.01 | 0.04 | 0.01 | 0.15 | 0.03 | 0.09 | 0.00 | 0.03 | 0.00 | 0.15 | 0.01 | 0.04 | 0.00 | 0.18 | 0.01 | 0.20 | 0.01 | 0.00 | 0.05 | 0.01 | 0.00 | 0.01 | 0.00 | 0.19 | 0.01 | 0.35 | 0.03 | 0.09 | 0.00 | 0.08 | 0.00 | 0.21 | 0.00 | 0.21 | 0.05 | 0.07 | 0.00 | 0.01 | 0.00 | 0.30 | 0.02 | 0.01 | 0.01 | 0.01 | 0.01 | 0.04 | 0.00 | 0.12 | 0.03 |
| PHF11 | ENSG00000136147 | 0.02 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.39 | 0.06 | 0.31 | 0.00 | 0.00 | 0.00 | 0.14 | 0.02 | 0.06 | 0.01 | 0.12 | 0.02 | 0.12 | 0.09 | 0.08 | 0.11 | 0.03 | 0.10 | 0.02 | 0.10 | 0.04 | 0.01 | 0.02 | 0.00 | 0.28 | 0.00 | 0.09 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.02 | 0.02 | 0.14 | 0.03 | 0.25 | 0.00 | 0.21 | 0.01 | 0.04 | 0.03 | 0.19 | 0.00 | 0.57 | 0.03 | 0.02 | 0.00 | 0.00 | 0.03 | 0.12 | 0.00 | 0.09 | 0.00 | 0.17 | 0.00 | 0.00 | 0.01 | 0.04 |
| TNS2 | ENSG00000111077 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.02 | 0.00 | 0.05 | 0.03 | 0.00 | 0.00 | 0.00 | 0.04 | 0.06 | 0.01 | 0.03 | 0.02 | 0.01 | 0.03 | 0.05 | 0.03 | 0.06 | 0.04 | 0.02 | 0.00 | 0.03 | 0.01 | 0.00 | 0.03 | 0.02 | 0.01 | 0.09 | 0.01 | 0.16 | 0.01 | 0.03 | 0.01 | 0.00 | 0.00 | 0.03 | 0.05 | 0.11 | 0.05 | 0.03 | 0.00 | 0.08 | 0.01 | 0.43 | 0.05 | 0.02 | 0.10 | 0.01 | 0.00 | 0.00 | 0.00 | 0.12 | 0.00 | 0.00 | 0.03 | 0.05 | 0.05 | 0.00 | 0.00 | 0.02 | 0.06 |
| PMS1 | ENSG00000064933 | 0.02 | 0.02 | 0.10 | 0.01 | 0.00 | 0.01 | 0.02 | 0.03 | 0.08 | 0.06 | 0.00 | 0.00 | 0.00 | 0.02 | 0.03 | 0.01 | 0.14 | 0.03 | 0.15 | 0.04 | 0.13 | 0.02 | 0.07 | 0.05 | 0.01 | 0.01 | 0.04 | 0.02 | 0.03 | 0.01 | 0.05 | 0.01 | 0.00 | 0.01 | 0.02 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.08 | 0.02 | 0.42 | 0.04 | 0.12 | 0.02 | 0.07 | 0.01 | 0.01 | 0.03 | 0.07 | 0.09 | 0.06 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.02 |
| MGMT | ENSG00000170430 | 0.00 | 0.02 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.07 | 0.04 | 0.10 | 0.00 | 0.05 | 0.02 | 0.15 | 0.04 | 0.05 | 0.05 | 0.08 | 0.02 | 0.04 | 0.05 | 0.08 | 0.07 | 0.07 | 0.01 | 0.06 | 0.02 | 0.06 | 0.01 | 0.03 | 0.02 | 0.11 | 0.14 | 0.17 | 0.11 | 0.02 | 0.02 | 0.02 | 0.00 | 0.00 | 0.07 | 0.11 | 0.26 | 0.21 | 0.02 | 0.05 | 0.05 | 0.06 | 0.09 | 0.04 | 0.09 | 0.07 | 0.05 | 0.08 | 0.00 | 0.00 | 0.03 | 0.03 | 0.01 | 0.13 | 0.00 | 0.07 | 0.00 | 0.00 | 0.01 | 0.05 |
| CPA6 | ENSG00000165078 | 0.00 | 0.01 | 0.00 | 0.01 | 0.06 | 0.00 | 0.06 | 0.01 | 0.09 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.14 | 0.02 | 0.10 | 0.02 | 0.05 | 0.01 | 0.11 | 0.00 | 0.08 | 0.01 | 0.06 | 0.00 | 0.15 | 0.03 | 0.01 | 0.02 | 0.08 | 0.01 | 0.06 | 0.02 | 0.02 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.22 | 0.02 | 0.39 | 0.07 | 0.04 | 0.01 | 0.07 | 0.01 | 0.25 | 0.06 | 0.20 | 0.04 | 0.19 | 0.00 | 0.01 | 0.00 | 0.04 | 0.03 | 0.00 | 0.01 | 0.00 | 0.02 | 0.22 | 0.00 | 0.07 | 0.01 |
| HSPA1B | ENSG00000204388 | 0.01 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.00 | 0.15 | 0.04 | 0.00 | 0.00 | 0.02 | 0.02 | 0.08 | 0.02 | 0.06 | 0.05 | 0.03 | 0.04 | 0.13 | 0.05 | 0.12 | 0.04 | 0.03 | 0.02 | 0.07 | 0.02 | 0.05 | 0.01 | 0.11 | 0.01 | 0.05 | 0.03 | 0.08 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.09 | 0.03 | 0.29 | 0.06 | 0.17 | 0.01 | 0.05 | 0.01 | 0.10 | 0.03 | 0.06 | 0.07 | 0.01 | 0.01 | 0.00 | 0.00 | 0.02 | 0.17 | 0.01 | 0.01 | 0.00 | 0.01 | 0.11 | 0.00 | 0.12 | 0.01 |
| MPHOSPH8 | ENSG00000196199 | 0.00 | 0.02 | 0.01 | 0.01 | 0.00 | 0.00 | 0.05 | 0.04 | 0.09 | 0.08 | 0.00 | 0.00 | 0.00 | 0.17 | 0.02 | 0.15 | 0.06 | 0.14 | 0.03 | 0.18 | 0.07 | 0.14 | 0.09 | 0.07 | 0.16 | 0.01 | 0.27 | 0.02 | 0.02 | 0.01 | 0.05 | 0.11 | 0.00 | 0.15 | 0.00 | 0.07 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.09 | 0.08 | 0.22 | 0.03 | 0.17 | 0.02 | 0.07 | 0.30 | 0.13 | 0.20 | 0.19 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.06 | 0.01 | 0.07 | 0.02 | 0.07 | 0.00 | 0.00 | 0.06 | 0.05 |
| PTPRF | ENSG00000142949 | 0.00 | 0.02 | 0.01 | 0.03 | 0.00 | 0.00 | 0.00 | 0.02 | 0.14 | 0.03 | 0.00 | 0.00 | 0.08 | 0.03 | 0.10 | 0.02 | 0.12 | 0.01 | 0.08 | 0.01 | 0.16 | 0.01 | 0.04 | 0.03 | 0.03 | 0.02 | 0.02 | 0.01 | 0.03 | 0.00 | 0.03 | 0.09 | 0.00 | 0.22 | 0.01 | 0.03 | 0.02 | 0.09 | 0.00 | 0.00 | 0.09 | 0.04 | 0.56 | 0.05 | 0.11 | 0.01 | 0.12 | 0.01 | 0.23 | 0.05 | 0.11 | 0.03 | 0.05 | 0.03 | 0.02 | 0.00 | 0.00 | 0.05 | 0.00 | 0.01 | 0.02 | 0.00 | 0.00 | 0.07 | 0.04 | 0.02 |
| OMA1 | ENSG00000162600 | 0.00 | 0.01 | 0.01 | 0.02 | 0.00 | 0.00 | 0.01 | 0.07 | 0.09 | 0.05 | 0.00 | 0.00 | 0.04 | 0.03 | 0.07 | 0.06 | 0.07 | 0.04 | 0.06 | 0.03 | 0.06 | 0.05 | 0.03 | 0.05 | 0.00 | 0.06 | 0.00 | 0.04 | 0.00 | 0.01 | 0.02 | 0.04 | 0.00 | 0.21 | 0.04 | 0.04 | 0.00 | 0.18 | 0.00 | 0.00 | 0.08 | 0.06 | 0.26 | 0.14 | 0.11 | 0.02 | 0.03 | 0.02 | 0.00 | 0.06 | 0.57 | 0.02 | 0.04 | 0.03 | 0.02 | 0.00 | 0.00 | 0.03 | 0.00 | 0.01 | 0.02 | 0.01 | 0.00 | 0.07 | 0.02 | 0.03 |
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