questions regarding GO enrichment analysis
Hello everyone,
I'm working on B.napus, and have conducted an RNA-seq via a company. In my hand here is a list of DEGs with B.napus official gene names (Bna....) , yet I don't have sequences of each of them and I would like to do GO enrichment analysis, what should I do? Should I firstly transfer the gene into counterparts in A.thaliana? and how can I do that?
many thanks in advance!
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citronxu •
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You don't need sequences for enrichment analysis. You can check agriGO for the enrichment analysis http://bioinfo.cau.edu.cn/agriGO/analysis.php which supports Brassica napus. Here the documentation http://bioinfo.cau.edu.cn/agriGO/manual.php
morning, thank you for the reply. But it seems IDs or gene names in my list are not included in the database, where first I should tranfer them into, for example, genBank IDs. But I don't know how to do it parallelly since I have almost 1000 genes.
You have to supply only your DEGs in section 2 (cause apparently GO is supported meaning already present associated in their database) and the whole genome functional annotation (ID + GO) in section 3 as your custom reference background. Carefully read the documentation.