Question

using other ontologies in topGO && building GO.db like database for GO-like ontologies

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Xin.H ▴ 10

@xinh-6443

Last seen 9.7 years ago

Hi, package : GO.db http://www.bioconductor.org/packages/release/data/annotation/html/GO.d b.html package : topGO http://www.bioconductor.org/packages/release/bioc/html/topGO.html I was using topGO for gene ontology analysis and was wondering if the same statics methods can be used on other ontologies such as Disease Ontology. Does anyone know how to configure topGO to accept customize ontologies? I also notices that topGO uses GO.db package to build the R object so it should be possible to build other ontology objects in topGO giving a similar XX.db file. I have done some search in the previous emails from the bioconductor email list and couldn't find any thing about building your own GO.db . So I was wondering if there is any thing available for converting an ontology file(e.g. .obo) into a XXX.db file that can be use in topGO? Many thanks, Xin [[alternative HTML version deleted]]

GO topGO GO topGO • 1.6k views

ADD COMMENT • link updated 6.4 years ago by Yvan Wenger ▴ 50 • written 10.2 years ago by Xin.H ▴ 10

score 0 · Answer 1 · 2017-12-25

Hello,

I have a similar question and was wondering if this could be solved. Basically I annotate my sequences with PANTHER13, retrieve GO annotations associated with Panther families and sub-families, and this is what I input to topGO using readMappings(). It seems to be ok, the analyses run fine, no errors, and the results seem to make sense so far. However, you would like to make a try with an ontology that is provided by Panther itself http://data.pantherdb.org/PANTHER13/ontology/PANTHERGOslim.obo.

Is there any way to do that? Basically I think that my question is the same than the one posted above, but as the number of downloads/users have bumped up since Xin's question, I decided to ask it again.

Many thanks !

Yvan