I have received RNA seq data from three KO mice and wild type mice. The mice are littermates from commom father and two mother and age of 2-month old. I got the RPKM values and performed GSEA analysis. But I am not getting heat map with clear distinction. The sequencing they performed were Single paired. Here i am attaching heatmap for the hallmark gene set. I am a non-bioinformatician , please provide suggestions.
You could check all your samples in a PCA like analysis to see how different are them. Instead of only showing the heatmap of some genes, you could in the first instance, generate the heatmap with all your genes, in order to see differences in abundances between the control vs wt. Maybe you could identify cluster of genes in which their abundances change berween these two condition. Finally, the best way to identify genes up/down-regulated in one or another condition is to perform a differential gene expression analysis.