Specific questions about pathway analysis

Question

[halo22]

Hello All,

I have a question regarding pathway analysis, your input on this is much appreciated. So I did an expression study for my normal and cancer population. I performed my univariate analysis, adjusted for multiple comparison and now I have a small list of genes that are significant. Next, I wanted to perform pathway analysis (mostly IPA) but I have very specific questions before proceeding.

1) Can I do IPA analysis by including the genes and their expression values to see if different pathways are involved in both my groups? 2) Is there a way to know if there are certain quantifiable differences or alternate pathways due to the changes in expression values?

Answer 1

[anp375]

1. • I think you need the genes and their differential expression p-values, not expression levels. I don't know for sure though.
2. • Normally, you're provided a list of multiple enriched pathways and associated enrichment p-values.