I'd like to correct for a biased gene enrichment analysis test.
Consider the following usual gene expression experiment: Consider a database D with N pathways having each {K1,....,Kn} genes. I did a gene expression experiment where the organism considered has L < N pathways having each {M1,...,Ml} < {K1,....,Kn} genes, and the relative proportion (representation) between pathways in L is different from N. e.g. Bateria B has 50 genes of a given pathway and 2 genes in the L-1 others. Database D has 100 genes in all pathways.
Doesn't that call for a correction? Isn't that most organisms analysed in gene expression assays have a different representation of pathways compared to the queried DB? If so how can I correct for it?
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Marouen Ben Guebila •
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You shouldn't need any correction because the DB has to be species specific (otherwise you wouldn't have gene to pathway mappings). Your gene enrichment testing is with respect to L and {M1, .., Ml} not N and {K1, ... , Kn}.