Hi friends,
I have some significantly differentially genes that are down regulated(negative fold change).
In the pathway analysis for these genes, is it correct interpretation to say that pathways related to these genes are downregulated in my samples as these genes are downregulated and in normal case if they were not down regulated they would be able to enrich the related significant pathways)
It only means that you might have something going on for that pathway in your data. What exactly is on you to figure out biologically. Say a pathway had 100 genes, and you find 10 of them being upregulated, but the molecular function of those 10 genes was to actually suppress (so negatively regulate) the pathway, then the pathway biologically would go down, even though these genes go up. Be careful with these enrichment tools, all they do is statistical enrichment analysis, the cell itself does not care about statistics. After DEG it requires biological knowledge of your system and downstream experiments to figure out the actual in vivo process. After all DEGs are just transcriptional, there is no guarantee this translates to actual protein activity changes in a pathway. Keep all that in mind.