ReactomePA::enrichPathway, how to avoid false discovery due to small number of gene set?

Question

[shoko1018]

Hi, I have a dataset where only two genes passed our significance cutoff. When I run enrichPathway in ReactomePA using those two genes as input for gene, it still gave me some 'significant' pathways. Here, this example has GeneRatio=1/1 and p.adjust<0.05.

Description GeneRatio BgRatio pvalue p.adjust
Cell surface interactions at the vascular wall 1/1 87/6902 0.0126050420168067 0.03781512605042

For this dataset, I would loose the filtering criteria to include larger number of genes to input in ReactomePA, but this made me wonder what is the optimal number of genes to input. Or if there's any way to avoid those false discoveries?

Answer 1

[Leite]

@shoko1018

There is no "optimal" number to put into the reactome. There are the number of genes you are working on and the program will return the results.

What you can try is to get more information from other banks, you could use the:

http://amp.pharm.mssm.edu/Enrichr/

[shoko1018]

Thank you. I will look into Enrichr as well.