KEGG Pathway analysis for non-model organism using goseq
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7 months ago
analyst ▴ 50

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

non-model-organism KEGG DEG • 860 views
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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

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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.

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