Question: Question about gene ontology data visualization
0
gravatar for soojinima
13 months ago by
soojinima10
soojinima10 wrote:

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. I used volcano plot to express it in R like this with gene annotation

ADD COMMENTlink modified 13 months ago by Pietro100 • written 13 months ago by soojinima10

Have a look at GOplot.

ADD REPLYlink modified 13 months ago • written 13 months ago by SMK1.9k
0
gravatar for Pietro
13 months ago by
Pietro100
Italy
Pietro100 wrote:

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:

test

With other visualization like bubble plot you would include other info as well, but in my opinion often too many info are confusing.

ADD COMMENTlink written 13 months ago by Pietro100

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

ADD REPLYlink written 13 months ago by soojinima10

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.

ADD REPLYlink written 13 months ago by Pietro100

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.

ADD REPLYlink written 5 months ago by Arindam Ghosh300
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