Gene ontology and KEGG pathway analysis of rice RNA-seq data

Question

[rj.rezwan]

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.

Answer 1

[pixie@bioinfo]

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/

[rj.rezwan]

Thanks for suggestion. I will consult from you, if I face any sort of confusion during analysis on mapman.

Answer 2

[Kevin Blighe]

Hi,

What about EasyGO or DAVID?

[rj.rezwan]

Hi, I will try these two online tools. Thanks.

[alaminzju]

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.

Answer 3

[alaminzju]

You can use agriGo v2.0 (http://systemsbiology.cau.edu.cn/agriGOv2/) for gene ontology analysis. It is very convenient and easy.

Answer 4

[Leite]

You can use Uniprot,

In this example I used Amborella trichopoda genes

upload pictures

Best regards,

Leite

Answer 5

[EagleEye]

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.

[afli]

The format of gene id and gene symbol is not very commonly used in rice, could you please modify gene id with the format like LOC_Os04g09010, that maybe more convenient for us to use.

[EagleEye]

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

[afli]

I see, thank you very much!