Question

Using goseq on non-model organism - how to define genome?

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Jon Bråte ▴ 260

@jon-brate-6263

Last seen 5 months ago

Norway

Hi,

I have a few questions about using goseq on a non-model organism:

I have a set of DE-genes identified by DESeq2 called genes,

a vector of gene lengths called lengthData created like this:

txdb = makeTxDbFromGFF("../merged_fixed.gtf", format = ("gtf"))
txsByGene=transcriptsBy(txdb,"gene")
lengthData=median(width(txsByGene))

And I have a reference set of genes called backM which is a list of gene names

I am at this point of the goseq manual:

pwf=nullp(genes,"hg19","ensGene")

And my question is how do I refer to my non-model genome and what should I provide as id?

Thanks, Jon

goseq go genesetenrichment • 5.4k views

ADD COMMENT • link updated 9.0 years ago by Gordon Smyth 52k • written 9.0 years ago by Jon Bråte ▴ 260

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Is your organism supported by Annotation Hub? Try:

library(AnnotationHub)
hub = AnnotationHub()
query(hub, c("OrgDb"))

ADD REPLY • link 8.9 years ago Gordon Smyth 52k

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No it's not, but thanks for the Annotation Hub tip! I haven't used if before.

ADD REPLY • link 8.9 years ago Jon Bråte ▴ 260

score 0 · Answer 1 · 2015-12-19

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Gordon Smyth 52k

@gordon-smyth

Last seen 2 minutes ago

WEHI, Melbourne, Australia

Initially I said "Obviously you cannot do a GO analysis for a species for which no GO database exists".

However later Steve Lianglou pointed out that you can do a goseq analysis of any species if you provide your own GO mapping. I was not familiar with this part of the goseq package, so you should follow Steve's suggestions below.

ADD COMMENT • link 9.0 years ago • updated 8.9 years ago Gordon Smyth 52k

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Ok, I see. So it is not possible to use goseq on organisms not in supporedGenomes()? From the manual I got the impression that if I supplied gene length information and the GO-mapping manually I could still run it?

ADD REPLY • link 9.0 years ago Jon Bråte ▴ 260

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You can. You will have to provide a mapping of your gene id's to go (or whatever) id's wired up in a data.frame, too. It's doable

ADD REPLY • link 9.0 years ago Steve Lianoglou ★ 13k

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Thanks! I have created such a mapping with Blast2GO. But I guess this is used in the goseq function?

For nullp() I just skipped providing "genome" and "id" and entered the lengthData as bias.data and it seems to work. I did actually read the nullp documentation before posting the question, but it was not so obvious to me that genome and id could be skipped.

ADD REPLY • link 9.0 years ago Jon Bråte ▴ 260

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Now that you have the output from nullp and the list of differentially expressed genes, you just need to create the gene2cat object for a call to goseq. The documentation in ?goseq describes the format reasonably well. It is of the format that is returned from the getgo function as well. You can look at the help in ?getgo (and run the example code there) to demystify that a bit further, if necessary.

ADD REPLY • link 9.0 years ago Steve Lianoglou ★ 13k