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!