GO enrichment analysis
1
0
Entering edit mode
14 months ago
hellokwmin • 0

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?

enter image description here

enrichment analysis GO • 798 views
ADD COMMENT
1
Entering edit mode

g:Profiler has an Arabidopsis option:

g:Profiler

ADD REPLY
0
Entering edit mode
14 months ago

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.

ADD COMMENT
0
Entering edit mode

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.

ADD REPLY
1
Entering edit mode

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

ADD REPLY

Login before adding your answer.

Traffic: 1536 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6