can you calculate GO enrichment from GO terms and IDs?

Question

[Emma]

Hey all,

I used the tool Pannzer to get GO information for my gene list in a non model species (monarch butterfly). I know Pannzer doesn't do enrichment analyses so I repeated using the whole monarch genome. Does anyone know a tool that accepts protein ID and corresponding GO terms for enrichment analysis rather than just a gene list from a limited number of species? If not, is there a way to do this analysis myself which doesn't involve going GO term by GO term?

thanks a lot.

[microfuge]

I generally use Agrigo (http://bioinfo.cau.edu.cn/agriGO/analysis.php) specializing on plants. But it does provide using your own annotation using the custom option. The outputs/plots are very good but never tried to use with a non plant species.

Answer 1

[Jean-Karim Heriche]

There are two approaches you can take:
- If you already have your genes annotated, you could simply do the enrichment tests yourself using the algorithm of your choice. At the most basic, you just need to build contingency tables and do Fisher's exact tests, correcting for multiple testing. This is easily done with a script. I think the Bioconductor package topGO also allows you to use your own annotation file.
- You can use orthologs of your genes in a species represented in available tools as proxy for the analysis.

Answer 2

[Guangchuang Yu]

clusterProfiler support using user's own annotation.

The package is quite popular and has been cited by >200 papers.

Answer 3

[EagleEye]

A: GO enrichment analysis using a Text file with all the genes and GO ids associat

Answer 4

[tarashanst]

This should do what you need