Plotting Gene Ontology analysis results and questions about Fold Enrichment and other parameters
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4 months ago
Raito92 ▴ 60

Hello everyone, I've performed a Gene Ontology analysis on a list of DEGs, and I obtained, as a result, a list of GO terms. For each term, it's shown how many times it's found in up and down-regulated genes. Two p-values, representing statistical significant for such findings, are given too.

I've used the function goana from limma in R Bioconductor.

Now I'm looking for a tool to create Gene Ontology plots.

To date, I've only created with Excel the classic 'bar plots', like these:

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However, I've noticed there are more complex types of plots, like the ones where GO terms are represented by circles, whose size is proportional to their up/down regulation. Here are a couple of examples.

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These plots refer to parameters not appearing in the results of my previous analysis, including a Fold enrichment, FDR and a z-score.

Is there any way to manually calculate Fold enrichment? Any suggestion in general about how to plot GO results starting from just the GO terms up and down counts and their p-values?

Thanks in advance for your help!

Ontology Enrichment Gene GO • 329 views

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