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Question about gene ontology data visualization

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

rna-seq go gene ontology visualization r
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updated by Pietro Pietro • written by soojinima • soojinima

Have a look at GOplot.

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written by AK AK

1 answer

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.

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written by Pietro Pietro

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

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written by soojinima • soojinima

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.

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written by Pietro Pietro

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.

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written by Arindam Ghosh Arindam Ghosh

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