Pathway analysis on specific genes

Question

[lornaas]

Is there a way to perform effectively a pathway analysis for specific set of genes?

I want to know if a group of genes, together, are signficantly different in a group of samples compared to controls. Similar to a pathway analysis, but these are a group of relatively under-studied genes and therefore the group doesn't appear in ordinary gene sets so I want to make my own group to test.

Thanks in advance

Answer 1

[Alex Reynolds]

You could do a hypergeometric test, but for a group of related (dependent) samples you may want to apply a multiple testing correction on the p-values you get back, such as Benjamini/Yekutieli controlling for an FDR threshold (e.g., 5%). Python is one way to do it. R is another.