Visualize Segmented CNV data
You can now view segmented copy number variation data in Xena! We have segmented CNV datasets for all TCGA cohorts, including Pan-Can, and ICGC cohorts too. Here are a few examples showing what you can do with this data:
TMPRSS2-ERG Fusion in TCGA Prostate Cancer
We can use the segmented CNV data to more closely examine the well-known TMPRSS2-ERG fusion in Prostate Cancer, where the oncogene ERG fuses to the TMPRSS2 promoter, driving over-expression of ERG (St. John 2012, Adamo 2016). We can see in columns D and E the specific break point in each gene and their relationship to over expression in ERG (column A). Looking more closely at which exons are over expressed, we can see that it is primarily in the 3' exons. Click on the image to explore more!
CDKN2A deletion in TCGA Glioblastoma
Using the segmented CNV dataset we can see the relationship between CDKN2A deletion and lowered CDKN2A expression in TCGA Glioblastoma. Click on the image to explore more!
To View Segmented CNV Data:
- Choose a TCGA or ICGC cohort
- Enter a gene, chromosome or chromosome segment that you wish to view.
- Click on 'Copy number' and click 'Done'
- If needed, enter a second variable and click 'Done'.