Hi, I am working on rice. I have a question here that which software is better for gene ontology and KEGG pathway analysis? I have already used "AgriGo" online tool for analysis, but it is giving error in bar (graphical) representation.
•
written
by
rj.rezwan •
You can use MapMan. I found that it has more gene annotations for rice than other tools. It has to be locally installed together with the specific annotation file for the species. More details here: https://mapman.gabipd.org/
Thanks for suggestion. I will consult from you, if I face any sort of confusion during analysis on mapman.
Hi, I will try these two online tools. Thanks.
I did not find any option for rice in DAVID database. So, I think DAVID is not appropriate database for GO and KEGG for rice RNA-Seq analysis.
Did you try EasyGO? If you additionally want to paste a short list of rice gene IDs, I will then try to find some tool for yo to use.
Kevin
You can use agriGo v2.0 (http://systemsbiology.cau.edu.cn/agriGOv2/) for gene ontology analysis. It is very convenient and easy.
Try GeneSCF:
For 'Oryza sativa japonica (Japanese rice) (RefSeq)' from KEGG: osa
./prepare_database -db=KEGG -org=osa
./geneSCF -m=normal -i=INPUTgene.list -t=sym -db=KEGG -o=/ExistingOUTPUTfolder/ -org=osa --plot=no --background=#num_genes
Alternate:
For 'Oryza sativa japonica (Japanese rice) (RAPDB)' from KEGG: dosa
./prepare_database -db=KEGG -org=dosa
./geneSCF -m=normal -i=INPUTgene.list -t=sym -db=KEGG -o=/ExistingOUTPUTfolder/ -org=dosa --plot=no --background=#num_genes
Check other KEGG organism/species codes here to use in GeneSCF.
Hi afli,
Thanks for you comment. Since geneSCF has to maintain some standard nomenclature, geneid always refers to Entrez geneid and anything other than entrezid (such as gene names containing characters rather than just numbers) must be considered as gene symbol.
Example: Oryza sativa japonica (Japanese rice)
Geneid GeneSymbol
9271090 TPRXL, LOC9271090
9271636 LOC9271636
107278145 OsI_030282, LOC107278145
Log in to answer this question.
