I have 13 clusters of co-expressed genes, obtained form an expression dataset of 6800 genes per 27 samples. Among the 6800 genes used for the netowrk analysis, 168 have a single SNPs (compared to the WT strain). I was wondering if an hypergeometric test can applied to find modules enriched with genes having a SNP:
Number of genes with SNP in the turquoise module 17 Total number of genes in the turquoise module 889 Total number of genes in the network 6800 Total number of genes with SNP 168 phyper(17-1,889,6800,168, lower.tail = TRUE, log.p = FALSE) #edited
Does it make any sense?