Question: Question about gene ontology data visualization
0
gravatar for soojinima
12 days 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 11 days ago by Pietro70 • written 12 days ago by soojinima10

Have a look at GOplot.

ADD REPLYlink modified 11 days ago • written 11 days ago by SMK1.8k
0
gravatar for Pietro
11 days ago by
Pietro70
Italy
Pietro70 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 11 days ago by Pietro70

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

ADD REPLYlink written 11 days 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 11 days ago by Pietro70
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