Hello, I would like to perform GO enrichment analysis. My data format after deseq analysis as following image which contains deseq-related factors and functional annotation (accession id based on nrdatabase as well as arabidopsis) also with GO id generated from interproscan.
with this information, which tools (e.g. R software or web-based anlyzer) can I use to perform GO analysis? or, do I need more information to conduct GO analysis other than factors present in image?
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hellokwmin •
You don't mention which organism are you using. If it is a model system, you only need to select the organism, and introduce the names of the genes of interest in http://geneontology.org/. Everything will be automatic for you with diverse options to choose.
Thank you for your reply. Unfortunately, the organism I am using is non-model organism (i.e. one of plant species). So, with the information I attached as image, Is there any way to do GO analysis? Thank you.
I had the same situation that I solved using the R package TopGO.
You have already the list of GO terms. Need to follow the instructions included in this package or within some other that are designed for this end
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g:Profiler has an Arabidopsis option:
g:Profiler