Gene ontology and KEGG pathway analysis of Oryza data

Question

[hafiz.talhamalik]

Hi, I am working on Oryza. I need to perform GO anotology and KEGG pathway analysis. I have used some online tools but now looking for some R, python or Linux-based tools. Is there any ? I checked geneSCF, but it doesn't support annotations for Oryza. Any help is highly appreciated

[Dunois]

eggnog-mapper and/or interproscan should do the trick for annotating GO and KEGG terms; both of these are command line tools. You should be able to tackle the enrichment analysis with clusterprofiler in R.

[hafiz.talhamalik]

does eggnog-mapper and interproscan allow you to make graphs ??

[Dunois]

No. They will only produce annotations as flat files. interproscan does produce some HTML output I think, but that's about it. That said, you're going to have to be most specific: what kind of "graphs" do you have in mind?

[naveedkhanchemist]

yes dear, I am also facing the same problem, did not find any proper r script for performing GO and KEGG analysis for rice (oryza sativa).

[jv]

As Dunois suggested, the R Bioconductor package clusterProfiler is a good option for gene set enrichment and over-representation testing within R. You can use this package for any organism. The generic enricher and GSEA functions can be used to test any user-defined gene sets: https://guangchuangyu.github.io/2015/05/use-clusterprofiler-as-an-universal-enrichment-analysis-tool/