DAVID enrichment analysis

Question

[sarahawan92]

I have performed the functional enrichment analysis of Upregulated genes by using DAVID online software. I have got the results in which P Values and adjusted Values are also given. If I looked at P values I can found many significant biological process and molecular functions but on other hand , if I looked at P.adjusted there is nothing significant in my data. I am confused that what should I have to do as I am working on Manuscript. Kindly give me some advise. Thanks!

Answer 1

[shiyang_bio]

In actual fact, from a statistical perspective, p.adjusted should be used. As you may do thousands of statistical tests, some pathways would pop up by random and seems "significant" and adjusting these p values can avoid such thing. However, to be honest, the non-adjusted p value is also widely used in publications. I think the main reason is, just as you said, using p.adjusted will dramatically reduce the number of enriched pathways, which makes it more difficult to tell a story or write an article. In all, my suggestion is, pvalue is also OK. From my experience, reviewers or editors won't challenge this point. BTW, you'd better to check something besides pvalue, such as the number of enriched genes in that pathway, or whether these genes play an important role in that pathway. Just to make sure this pathway will be actually affected by your gene list. Hope this will help you.

[sarahawan92]

Thanks. I am also thinking to look at the gene functions as by looking at P.adjusted values I have nothing significant.