KEGG Pathway analysis for non-model organism using goseq
Dear all,
I have to perform KEGG Pathway analysis of wheat DEGs (differentially expressed genes). I found goseq in R but wheat is not native organism. For GO term analysis of wheat I first retrieved GO term IDs from biomart and then fed to goseq function but I did not find KEGG in biomart. How can I get KEGG ontologies?
Anyone please suggest how can I perform KEGG Pathway analysis for non-native organism's genes.
Thanks
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Bushra Bibi
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You need to use KEGGREST to retrieve the KO for wheat. See this question for more details: KEGG pathways associated to a gene using BiomaRt
Thanks Mark I tried this thread. For short list of genes it worked well but gave timeout error for larger list (containing thousands of genes). I used enrichKEGG it worked for larger list.