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 |
| SLC22A15 | ENSG00000163393 | 0.00 | 0.63 | 0 | 4 |
| HDAC4 | ENSG00000068024 | 0.00 | 2.07 | 0 | 8 |
| CD46 | ENSG00000117335 | 0.12 | 0.00 | 1 | 0 |
| NTNG1 | ENSG00000162631 | 0.00 | 0.00 | 0 | 0 |
| ADGRV1 | ENSG00000164199 | 0.00 | 0.00 | 0 | 0 |
| HDAC2 | ENSG00000196591 | 0.00 | 0.41 | 0 | 3 |
| ACAN | ENSG00000157766 | 0.00 | 0.00 | 0 | 0 |
| CSNK1A1 | ENSG00000113712 | 0.30 | 0.14 | 1 | 1 |
| ITGA3 | ENSG00000005884 | 0.00 | 0.00 | 0 | 0 |
| SLC6A19 | ENSG00000174358 | 0.00 | 0.00 | 0 | 0 |
| BPTF | ENSG00000171634 | 0.99 | 0.00 | 5 | 0 |
| CDC14A | ENSG00000079335 | 0.00 | 0.62 | 0 | 3 |
| BIRC2 | ENSG00000110330 | 1.55 | 0.17 | 4 | 1 |
| CHST12 | ENSG00000136213 | 0.59 | 0.40 | 4 | 1 |
| IL1R1 | ENSG00000115594 | 0.00 | 0.00 | 0 | 0 |
| UBA2 | ENSG00000126261 | 0.00 | 0.00 | 0 | 0 |
| NOTCH1 | ENSG00000148400 | 0.00 | 0.23 | 0 | 1 |
| THBS1 | ENSG00000137801 | 0.00 | 0.00 | 0 | 0 |
| PTPRR | ENSG00000153233 | 0.00 | 0.00 | 0 | 0 |
| RANBP2 | ENSG00000153201 | 0.00 | 0.00 | 0 | 0 |
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