Which tool is most popular for GO over-representation analysis?

Question

[dcheng1]

I noticed GO consortium use PANTHER on their website. So it looks like PANTHER is a very official tool. I'm wondering why not everyone using it. Is there a reason for not using PANTHER?

[Kevin Blighe]

There are probably hundreds of GO enrichment tools. People use Panther, but you can use anything that you want.

Answer 1

[Jean-Karim Heriche]

You should make a distinction between the tools that are software implementation of analysis methods and the source of the annotation data used by the tools. In this context, PANTHER is not a tool, it's a data resource used as source of annotations. You can use PANTHER data with many tools/methods that do over-representation analysis. One such tool is implemented on the PANTHER website. There are many sources of annotations and they differ by the type of entities that they annotate (e.g. genes, proteins...) and how they group these entities. People use the data sources that contains information relevant to their question and/or that is more convenient to use.

Answer 2

[Min Dai]

You can try Metascape, which is online and easy-to-use. Besides, you can visualise the enriched GO terms by dot plot in R using ggplot2.

Answer 3

[Shalu Jhanwar]

There are many tools available to perform GO analysis. The choice of tools may depend upon

1. if the tool is dedicated to performing analysis for certain species.

2. how frequently the datasets/databases used by the tools are updated. That will affect the results and conclusions a lot. Have a look at the comparison of the tools/data resources at here.

Also benchmarking with the recently developed GO tools can help understand the pros and cons of using specific tools (e.g. Toward a gold standard for benchmarking gene set enrichment analysis).