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 |
| CHEK1 | ENSG00000149554 | 0.00 | 1.02 | 0 | 5 |
| KLF5 | ENSG00000102554 | 0.50 | 0.27 | 2 | 1 |
| AURKB | ENSG00000178999 | 0.00 | 0.00 | 0 | 0 |
| TYMS | ENSG00000176890 | 0.18 | 0.12 | 1 | 1 |
| AURKA | ENSG00000087586 | 0.12 | 0.00 | 1 | 0 |
| ESR1 | ENSG00000091831 | 0.00 | 0.00 | 0 | 0 |
| ERG | ENSG00000157554 | 0.00 | 0.00 | 0 | 0 |
| CDK1 | ENSG00000170312 | 0.00 | 0.00 | 0 | 0 |
| JAK2 | ENSG00000096968 | 0.59 | 0.31 | 3 | 2 |
| KIT | ENSG00000157404 | 0.13 | 0.00 | 1 | 0 |
| PIK3CA | ENSG00000121879 | 0.48 | 0.00 | 2 | 0 |
| FGFR4 | ENSG00000160867 | 0.34 | 0.00 | 1 | 0 |
| KIF11 | ENSG00000138160 | 0.00 | 0.33 | 0 | 1 |
| TP63 | ENSG00000073282 | 0.00 | 0.00 | 0 | 0 |
| CCND1 | ENSG00000110092 | 6.62 | 0.00 | 8 | 0 |
| MITF | ENSG00000187098 | 0.37 | 0.00 | 1 | 0 |
| PLK1 | ENSG00000166851 | 0.00 | 0.00 | 0 | 0 |
| EEF2 | ENSG00000167658 | 0.00 | 1.16 | 0 | 3 |
| GNAS | ENSG00000087460 | 0.26 | 0.00 | 1 | 0 |
| BRCA1 | ENSG00000012048 | 0.00 | 0.31 | 0 | 2 |
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