Entering edit mode
2.3 years ago
Rob
▴
170
Hi friends I have 120 patients and 19000 genes and I have differential expression analysis with DESeq2 in R. I found 213 significant genes. but when I send this to gene set enrichment analysis (GSEA) and pathway analysis I dont get any significant pathway and gene set. How can I interpret this? isnot it because maybe something is wrong that I even though I have significant differentialy expressed genes but not sig pathway and gene set?
how can I explain these ?
Your question is similar to: "I have a lot of data but no result. What does this mean?" Without more information, or knowing what you already expect from your data, it's hard to say anything meaningful. What hypothesis is your data testing? Do any of the genes you are getting support or disprove any hypothesis you can formulate? You have 120 patients - but are they divided into any sport of groupings? Are they for any particular tissue? You have significant genes by what criteria? Can you relax those criteria to get a larger set of genes? (200 is not that many for an enrichment analysis). What if you examined the top 500 as ranked by p-value? Is any of your patients or samples a positive control?
Hi seidel I have two groups of patients with and without a feature. I expect to get different pathways and gene sets upregulated/enriched for these.
for pathway analysis I used significant genes but for GSEA I used whole coding genes. it is weird for me that I dont get sig pathway and enriched gene set. I dont know how relate this to significant differential genes
You have 213 genes. You did pathway analysis on those genes and didn't find anything. Those are your results.
How can you interpret it? There's insufficient evidence that those 213 genes are enriched in any annotated pathway in whatever pathway database you're using. Simple as that.
Are those 213 genes related in function? They may or may not be; but based on your pathway analysis (using the criteria/thresholds you defined), you just couldn't find any evidence for it. Simple as that.
Awesome! Thank you so much for great short&concise answer dsull.