Question

Go term enrichemnt

1

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10.5 years ago

mileti.enrichetta ▴ 10

Hi,

I need a tool or a python library for GO term enrichment.

The problem is that I have Uniprot ID, in my dataset are present different species and in my analysis I don't want to discriminate between species.

Thanks

GO UniprotKB • 2.3k views

ADD COMMENT • link 10.5 years ago by mileti.enrichetta ▴ 10

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No, I don't want to find the respectively GO terms. I have yet the GO terms related to my Uniprto ID. I want to make a enrichment analysis on these

ADD REPLY • link 10.5 years ago by mileti.enrichetta ▴ 10

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So your question can be restated as, "How might I determine the background set of IDs to use to determine if those that I've found are enriched for GO categories?" If that's the case, then we'd need to know more about how the design of your experiment.

ADD REPLY • link 10.5 years ago by Devon Ryan 104k

Ram · Answer 1 · 2014-05-23

Hi,

It looks like you are trying to annotate the De-novo assembled transcripts. And you have Uniprot ID's which are heterogeneous (Homology Based Annotation - Annotated from various species). GO Mapping can be done using Simple Unix Commands, such as sort/join.

Download the ID Mapping file from Uniprot: here, in this file 1st & 2nd columns contains Uniprot AC/ID respectively and 7th GO IDs. That's it simply sort and join the files. QuickGO is an option, but it takes only one ID at time.

Good Luck