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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| Overall_Gscore | No. of Cancer Types | ||||
| HGNC Symbol | Ensembl Gene ID | Amplification | Deletion | Amplification | Deletion |
| C10orf54 | ENSG00000107738 | 0.00 | 0.00 | 0 | 0 |
| ABCC10 | ENSG00000124574 | 0.31 | 0.00 | 2 | 0 |
| ABHD16A | ENSG00000204427 | 0.00 | 0.00 | 0 | 0 |
| L3MBTL2 | ENSG00000100395 | 0.33 | 0.00 | 1 | 0 |
| MCOLN1 | ENSG00000090674 | 0.00 | 0.00 | 0 | 0 |
| MTMR1 | ENSG00000063601 | 0.16 | 0.00 | 1 | 0 |
| PRPSAP1 | ENSG00000161542 | 0.94 | 0.00 | 4 | 0 |
| ABCB11 | ENSG00000073734 | 0.00 | 0.00 | 0 | 0 |
| SULF2 | ENSG00000196562 | 0.12 | 0.00 | 1 | 0 |
| C1S | ENSG00000182326 | 0.00 | 0.00 | 0 | 0 |
| IVNS1ABP | ENSG00000116679 | 0.00 | 0.00 | 0 | 0 |
| PHF11 | ENSG00000136147 | 0.00 | 0.35 | 0 | 2 |
| TNS2 | ENSG00000111077 | 0.00 | 0.00 | 0 | 0 |
| PMS1 | ENSG00000064933 | 0.12 | 0.00 | 1 | 0 |
| MGMT | ENSG00000170430 | 0.00 | 0.11 | 0 | 1 |
| CPA6 | ENSG00000165078 | 0.00 | 0.00 | 0 | 0 |
| HSPA1B | ENSG00000204388 | 0.00 | 0.00 | 0 | 0 |
| MPHOSPH8 | ENSG00000196199 | 0.00 | 0.66 | 0 | 4 |
| PTPRF | ENSG00000142949 | 0.00 | 0.00 | 0 | 0 |
| OMA1 | ENSG00000162600 | 0.00 | 0.00 | 0 | 0 |
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