Create my own universel GO db from QuickGO in R

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4.0 years ago

Chvatil ▴ 130

Hello everyone, I would like to perform a term Go enrichment analysis of a sub dataset and for that I would like to use the R software.

And I have a few questions:

First of all I need to create my own universal data set (in other words a null distribution of all my known GO terms in the studied organism).

For this I go to https://www.ebi.ac.uk/QuickGO/ where I just have to enter the taxonomic identifier of the organism.

But I don't really know what to do with this then, here is a result for the mouse: https://www.ebi.ac.uk/QuickGO/annotations?taxonId=10090&taxonUsage=descendants

How to download all this (it says export but the maximum possible is 50,000), and especially how to build my universal database in R with this dataset, with TopGO for example?

Thank you for your advices and helps.

GO ontology R • 1.4k views

ADD COMMENT • link 4.0 years ago by Chvatil ▴ 130

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Hello Darill!

It appears that your post has been cross-posted to another site: https://bioinformatics.stackexchange.com/questions/13024/create-my-own-universel-go-db-from-quickgo-in-r

This is typically not recommended as it runs the risk of annoying people in both communities.