what are gene ratio and bg ratio in differentially expressed gene enrichment analysis?

Question

[tuf58502]

I got some differentially expressed genes after RNA-seq and Deseq2 normalization and I want to know their functions in some specific pathways. I uploaded the data on GO, KEGG and Reactome and I got some results of gene ratio, bg ratio and count. What does these terms mean and how can I use these data to explain whether one gene is related to a specific pathway or not? Can someone give me an example? Thanks so much!

Answer 1

[Kristoffer Vitting-Seerup]

You need to look for the enrichment score typically given as an odds ratio. And naturally you also need to consider the statistical test. If you want more help you need to upload an example of the result (and more info on how you did the analysis - which webside/tool did you use etc)

[tuf58502]

![data example][1] [1]: https://ibb.co/hkxsPH

![KEGG pathway plot][2] [2]: https://ibb.co/fOxyyc

After I used clusterProfiler to analyze my data, I got something like the image 1. I also did it on GO, Reactome and KEGG, I still got the similar data set with gene ratio, bg ratio and count. I can get the pathway plot from KEGG like the image 2. What they confuse me are the gene ratio and the bg ratio. I don't know which part represent my differentially express genes and which part represent the reference pathway in the database. Can you help me with that? Thanks!