Does My Gene of Interest Affect Survival?
Xena can be used to show whether any genomic or phenotype data significantly affects survival using our Kaplan Meier analysis.
IDH1 is an enzyme that affects metabolism in tumors and is frequently mutated in Lower Grade Glioma.
The column of data above shows mutations in IDH1 with the transcript along the top, with alternating light and dark gray exons. Mutations are colored by their functional impact, with mutations predicted to not make a protein in red, mutations predicted to make a protein but perhaps with altered function in blue and synonymous mutations in green. This mutation pattern is indicative of a hotspot.
Running a KM analysis, we can see a significant survival difference between samples with a mutation and those without.
Go to our Visualization tab at the top of the page.
Select the TCGA Lower Grade Glioma cohort
Select the Somatic Mutation SNPs and small INDELs (Broad automated) dataset.
Enter the gene 'IDH1'
Click the caret menu at the top of the column and select 'KM plot'.
Note that there is a '!' warning at the top of the plot indicating that some samples are in the plot twice (normal, recurrent tumor, metastasis, etc). To remove duplicate samples, please see our help page.
Custom grouping: only high and low expression groups
The default expression KM grouping is high, medium and low. How do I create a KM Plot with two groups: high and low expression? Read here
How to remove duplicate samples?
Have you ever noticed the warning icon in the top corner of a KM plot? Read here