Question: GOseq with non-supported organism
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gravatar for Jautis
22 months ago by
Jautis290
United States
Jautis290 wrote:

Hi, I want to do GO analsis on a set of differentially methylated genes (I have the ENSEMBL identifier for each gene). I did an initial analysis using ClueGO (implemented within Cytoscape), but want to do a followup using GOseq (the R package). This is because different number of CpG sites/tests per gene can lead to biases in GO analyses (Geeleher et al. 2013, bioinformatics).

However, my organism isn't supported in GOseq, meaning I need to import a file connecting ENSEMBL gene identifiers with GO categories. According to the GOseq manual, "The relationship between gene identifier and GO category can usually be obtained from the Gene Ontology website www.geneontology.org) or from the NCBI.". However. our organism is not listed on the downloads page for geneontology.org and I'm unable to find the proper location to download these associations from at NCBI.

Could anyone point me to the right place? Thanks!

go goseq R • 1.2k views
ADD COMMENTlink written 22 months ago by Jautis290
1

What is the organism? Did you try annotating with biomaRt?

https://bioconductor.org/packages/devel/bioc/vignettes/biomaRt/inst/doc/biomaRt.html#annotate-a-set-of-entrezgene-identifiers-with-go-annotation

ADD REPLYlink written 22 months ago by h.mon30k

We're working with the anubis baboon (genome Panu2.0). But thank you! I hadn't seen the biomaRt annotation tools

ADD REPLYlink written 22 months ago by Jautis290
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