Question: Gene ontology and KEGG pathway analysis of rice RNA-seq data
0
gravatar for rj.rezwan
2.7 years ago by
rj.rezwan0
rj.rezwan0 wrote:

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 • 2.7k views
ADD COMMENTlink modified 2.6 years ago by EagleEye6.6k • written 2.7 years ago by rj.rezwan0
3
gravatar for pixie@bioinfo
2.7 years ago by
pixie@bioinfo1.4k
pixie@bioinfo1.4k wrote:

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 written 2.7 years ago by pixie@bioinfo1.4k

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

ADD REPLYlink modified 2.7 years ago • written 2.7 years ago by rj.rezwan0
1
gravatar for Kevin Blighe
2.7 years ago by
Kevin Blighe61k
University College London
Kevin Blighe61k wrote:

Hi,

What about EasyGO or DAVID?

ADD COMMENTlink written 2.7 years ago by Kevin Blighe61k

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

ADD REPLYlink modified 2.7 years ago • written 2.7 years ago by rj.rezwan0

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 written 2.6 years ago by alaminzju0
0
gravatar for alaminzju
2.6 years ago by
alaminzju0
alaminzju0 wrote:

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

ADD COMMENTlink written 2.6 years ago by alaminzju0
0
gravatar for Leite
2.6 years ago by
Leite1000
São Paulo - Brazil - Unifesp
Leite1000 wrote:

You can use Uniprot,

In this example I used Amborella trichopoda genes

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Best regards,

Leite

ADD COMMENTlink modified 2.6 years ago • written 2.6 years ago by Leite1000
0
gravatar for EagleEye
2.6 years ago by
EagleEye6.6k
Sweden
EagleEye6.6k wrote:

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 modified 2.6 years ago • written 2.6 years ago by EagleEye6.6k

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 written 21 months ago by afli190
1

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 written 21 months ago by EagleEye6.6k

I see, thank you very much!

ADD REPLYlink written 20 months ago by afli190
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