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Gene ontology and KEGG pathway analysis of rice RNA-seq data
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3.2 years ago
rj.rezwan • 0
@rj.rezwan41599

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.

RNA-Seq • 1.9k views
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3.3 years ago
pixie@bioinfo ♦ 1.4k
@pixie@bioinfo329

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/

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

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3.3 years ago
@Kevin Blighe41557

Hi,

What about EasyGO or DAVID?

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

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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.

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3.2 years ago
alaminzju • 0
@alaminzju42921

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

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3.2 years ago
Leite • 400
@Leite31525

You can use Uniprot,

In this example I used Amborella trichopoda genes

Sem_t_tulo
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Best regards,

Leite

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3.2 years ago
EagleEye 6.4k
@EagleEye12958

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.

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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.

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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
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I see, thank you very much!

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