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 |
| RPS6KA5 | ENSG00000100784 | 0.00 | 0.00 | 0 | 0 |
| ITPR2 | ENSG00000123104 | 0.60 | 0.00 | 1 | 0 |
| EGF | ENSG00000138798 | 0.00 | 0.00 | 0 | 0 |
| COL14A1 | ENSG00000187955 | 0.00 | 0.00 | 0 | 0 |
| GLI2 | ENSG00000074047 | 0.32 | 0.00 | 1 | 0 |
| SLC4A5 | ENSG00000188687 | 0.00 | 0.00 | 0 | 0 |
| CILP | ENSG00000138615 | 0.00 | 0.00 | 0 | 0 |
| CPS1 | ENSG00000021826 | 0.00 | 0.00 | 0 | 0 |
| NUP210 | ENSG00000132182 | 0.00 | 0.18 | 0 | 1 |
| ABCB4 | ENSG00000005471 | 0.00 | 0.00 | 0 | 0 |
| COL23A1 | ENSG00000050767 | 0.33 | 0.12 | 1 | 1 |
| CCR7 | ENSG00000126353 | 0.00 | 0.00 | 0 | 0 |
| CPT1C | ENSG00000169169 | 0.00 | 0.33 | 0 | 1 |
| UGT2B4 | ENSG00000156096 | 0.00 | 0.00 | 0 | 0 |
| MYLK2 | ENSG00000101306 | 0.00 | 0.00 | 0 | 0 |
| IL4I1 | ENSG00000104951 | 0.00 | 0.00 | 0 | 0 |
| CASP8 | ENSG00000064012 | 0.00 | 0.00 | 0 | 0 |
| SDC2 | ENSG00000169439 | 0.57 | 0.00 | 2 | 0 |
| AZU1 | ENSG00000172232 | 0.00 | 0.00 | 0 | 0 |
| TRIM28 | ENSG00000130726 | 0.14 | 0.77 | 1 | 3 |
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