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

ADD COMMENTlink 2.3 years ago rj.rezwan • 0 • updated 2.2 years ago EagleEye 6.4k
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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/

ADD COMMENTlink 2.3 years ago pixie@bioinfo ♦ 1.4k
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Thanks for suggestion. I will consult from you, if I face any sort of confusion during analysis on mapman.

ADD REPLYlink 2.3 years ago
rj.rezwan
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Hi,

What about EasyGO or DAVID?

ADD COMMENTlink 2.3 years ago Kevin Blighe 43k
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Hi, I will try these two online tools. Thanks.

ADD REPLYlink 2.3 years ago
rj.rezwan
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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.

ADD REPLYlink 2.2 years ago
alaminzju
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You can use agriGo v2.0 (http://systemsbiology.cau.edu.cn/agriGOv2/) for gene ontology analysis. It is very convenient and easy.

ADD COMMENTlink 2.2 years ago alaminzju • 0
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You can use Uniprot,

In this example I used Amborella trichopoda genes

Sem_t_tulo
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Best regards,

Leite

ADD COMMENTlink 2.2 years ago Leite • 400
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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.

ADD COMMENTlink 2.2 years ago EagleEye 6.4k
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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.

ADD REPLYlink 16 months ago
afli
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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
ADD REPLYlink 16 months ago
EagleEye
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I see, thank you very much!

ADD REPLYlink 15 months ago
afli
• 180

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