I analysed GEO database about my research fields. I want to use these results for validating my data. I filtered gene list and gene ontology analysis was performed using David's functional annotation tool. I confirmed that the specific pathway I thought was equally activated in the experimental set of the same concept as me. I would like to inquire about how to visualize the gene list involved in this pathway. I used volcano plot to express it in R, but I ask if there is a better way for others to understand.
There are several ways to visualize the results of a functional annotation. Also depending of the type of analysis performed.
With the results of a Gene Ontology enrichment analysis I like a simple and elegant bar plot with -log10 of the adjusted pvalue on the x axis, like this:
With other visualization like bubble plot you would include other info as well, but in my opinion often too many info are confusing.