Question about gene ontology data visualization

Question

[soojinima]

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.

[AK]

Have a look at GOplot.

Answer 1

[Pietro]

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.

[soojinima]

Thank you for your kindly answer. But I actually want to visualize just one GO pathway and included gene.

[Pietro]

Then maybe you could draw a network of the pathway with Cytoscape and highlight your genes with colors corresponding to maybe fold change or pvalue from an enrichment test.

[Arindam Ghosh]

For my gene set I got ~160 terms from PANTHER. How do I display this? Should I show only the top 10 sorted by p-value? Have seen this , but not sure if this is logcal.