I am using iDEP software (http://bioinformatics.sdstate.edu/idep/) to do pathway analysis and gene enrichment analysis. I have gone through the userguide they provided for iDEP. I have also run GSEA with my entire gene list.
What I couldn't understand is how to interpret the results from iDEP and GSEA. What does the iDEP/ GSEA results/ graphs give us? I need to find differentially regulated pathways, bioenergetics pathway, mitochondrial pathway. I need to find the genes involved in these pathway and are differentially expressed genes. How do I do that? How do I get differentially regulated pathways from iDEP/ GSEA?
Any help is much appreciated.