I have RNA-seq data for two cell conditions. I want to test a hypothesis that there are more significantly upregulated genes in a given group (~1000 genes) versus all signficantly differentially expressed genes genomewide (~7000 genes).
Say, the subset of interest contains X genes, including X1 upregulated and X2 downregulated. The total genes subset contains Y genes, including Y1 upregulated and Y2 downregulated. How to calculate the P value? I am looking for a simple equation.
P.S. Previous testing of this hypothesis based on quantitative tests (comparing log2 fold changes) was not very successful, resulting in a statistically significant but quite a small difference of about 0.2-0.3 on the log2 scale (see details in the previous thread here). However, there is a very large difference in the numbers of genes which become upregulated in a given subset versus all genes.