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 |
| AKR1D1 | ENSG00000122787 | 0.00 | 0.00 | 0 | 0 |
| CACNG1 | ENSG00000108878 | 0.00 | 0.00 | 0 | 0 |
| MPST | ENSG00000128309 | 0.00 | 0.00 | 0 | 0 |
| C1QC | ENSG00000159189 | 0.00 | 0.00 | 0 | 0 |
| PTPN9 | ENSG00000169410 | 0.12 | 0.00 | 1 | 0 |
| NEK9 | ENSG00000119638 | 0.00 | 0.50 | 0 | 3 |
| INTS12 | ENSG00000138785 | 0.00 | 0.13 | 0 | 1 |
| GLYR1 | ENSG00000140632 | 0.00 | 0.12 | 0 | 1 |
| ADGRA3 | ENSG00000152990 | 0.00 | 0.00 | 0 | 0 |
| GSK3B | ENSG00000082701 | 0.00 | 0.00 | 0 | 0 |
| MINPP1 | ENSG00000107789 | 0.00 | 0.30 | 0 | 1 |
| NMT2 | ENSG00000152465 | 0.00 | 0.00 | 0 | 0 |
| TRIM21 | ENSG00000132109 | 0.00 | 0.00 | 0 | 0 |
| EHMT2 | ENSG00000204371 | 0.00 | 0.17 | 0 | 1 |
| NUCB2 | ENSG00000070081 | 0.00 | 0.00 | 0 | 0 |
| KLHL2 | ENSG00000109466 | 0.00 | 0.00 | 0 | 0 |
| PCCB | ENSG00000114054 | 0.00 | 0.00 | 0 | 0 |
| LTA4H | ENSG00000111144 | 0.00 | 0.00 | 0 | 0 |
| PHF20 | ENSG00000025293 | 0.00 | 0.00 | 0 | 0 |
| PHKG2 | ENSG00000156873 | 0.24 | 0.00 | 2 | 0 |
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