I would like to sort the TCGA dataset based on the expression of a panel of genes (let's say 22 genes related to the inflammatory response) on cBioportal to classify them as inflammatory-high and inflammatory-low.
Further, I would like to analyze the expression levels of gene of interest (for example VEGFA) among the inflammatory-high and inflammatory-low subgroups.
Any help would be highly appreciated...
Thank you,
Goutham
Hi Goutham Hv
I have some basic idea regarding that. You can take out patient data from the TCGA data servers. Sort down the data for those specific genes, do a clustering (please check which type will be suited for you, theoretically it should be median centric for each gene's expression). This will sort your samples to a ranked profile where each sample (patient) is ranked based on each gene expression compared to other samples and sum of ranks will be the sorting criteria. Just a theoretical framework. Hopefully it helps. suggestions are welcomed.
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