I have done the DEG analysis of RNA Seq by edge R software. I have a list of genes that have adjusted p values and log fold change 1.5. Upregulated genes are 2000 and downregulated are 1800. Now I am confused that should I used all the UP and down regulated genes for further DAVID and PPI analysis? Kindly give me some suggestions.
You can use the lists of up and down-regulated genes for over-representation analysis (ORA) in DAVID. Looking at enriched pathways or biological processes within these lists can give you an idea of what to look into further.
Since you also have the relative expression values, you can also use gene set enrichment analysis (GSEA) of the entire DEG list. This is a bit better than simple over-representation analysis since it also preserves the directionality of the expression change.
My preferred tool for doing quick exploratory analysis on DEG lists is Webgestalt (http://www.webgestalt.org/). The website lets you run ORA, GSEA, and network topology analyses using a variety of reference databases.
For further analysis, you can increase the cutoff values. I would take 2-fold change and 0.01 adjp to further narrow down, if your current list is bigger. Other-wise making sense of the PPI analysis would become extremely difficult.
Anukana Bhattacharjee Thanks for your reply. This is the same thing I was thinking as list is huge.
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