How to perform GO and Pathway analysis in plant?

Question

[Whoknows]

Hi friends,

I'm working on a data from shotgun proteomics (brassica napus specie). For GO and Pathway analysis I have problem because I could not find any good website or tool for functional annnotation.

I'd appreciate if someone help me to find a good tool/website for this purpose.

Tnx.

[Guangchuang Yu]

clusterProfiler may helps.

Answer 1

[EagleEye]

Linux based tool:

You can try GeneSCF (no installation required and simple to use).

Note: GeneSCF tool is GENE based, not protein based tool. If you got Uniprot Ids convert then to Entrez Gene (GeneIDs)/Gene name using http://www.uniprot.org/uploadlists/ . Then use it as input for GeneSCF.

KEGG pathway analysis for Brassica napus ( bna ) using GeneSCF:

./geneSCF -m=update -i=INPUTgene.list --gtype=gid -db=KEGG -o=/ExistingOUTPUTfolder/ -org=bna --plot=yes --background=1000

Input file (INPUTgene.list):

List of genes to be used for enrichment analysis in a plain text file (one per line).

Parameters to be changed according to your analysis:

--background=1000 (Please change this to total number of genes taken in your analysis/annotation)

--gtype=gid ('gid', for NCBI entrez gene ids and 'sym' for official gene symbols)

-o=/ExistingOUTPUTfolder/ (Folder where the output to be stored- NOT file name)

Web based tool:

Since GeneSCF uses geneontology.org as source, it does not cover ontology terms for Brassica napus but you can try this web based tool,

http://bioinfo.cau.edu.cn/agriGO/analysis.php

I hope this helps !

[Whoknows]

It was great and helpful dude.

[WouterDeCoster]

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