Question: Which statistical test to show the overlap of some genes in two different data is significant.
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archisman • 0 wrote:
Suppose I have a gene list of 470 genes that are induced in my study. I found that in other studies people already showed about 1000 genes were involved in the same kind of pathways but with the different model systems. Now, when I did an overlap of those 1000 genes with my 470 genes I found out of 470, at least 165 are common. Which statistical test I need to perform here to show that the overlap is not due to only by chance.
I suggest LOLA (BioC package) for this task: https://bioconductor.org/packages/release/bioc/html/LOLA.html
Hypergeometric test? See: Hypergeometric {stats}