Question

Pathway Enrichment

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2.6 years ago

SKY ▴ 60

Is there any tool that can directly give me my gene id in first column and its pathway in second column? i am working with rice gene id.

Thanks!

KEGG ORA ENRICHMENT PATHWAY • 1.6k views

ADD COMMENT • link updated 2.5 years ago by GenoMax 148k • written 2.6 years ago by SKY ▴ 60

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Check out this repo: https://github.com/hamidghaedi/keggPath2Gene_Path2Modules. I wrote this for human genes, you might be able to modify it based on your need.

ADD REPLY • link 2.6 years ago by Hamid Ghaedi 3.3k

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thank you. will try and get back.

ADD REPLY • link 2.6 years ago by SKY ▴ 60

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What is its pathway? One gene can be involved in a variety of processes. Enrichment usually means that you want to see whether processes are overrepresented in a group of genes. Can you elaborate and give an example what you need?

ADD REPLY • link 2.6 years ago by ATpoint 86k

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KEGG and/or reactome pathway. something like this...

Os01g0100100    pathway1
Os01g0100200    pathway1
Os01g0100300    pathway2
Os01g0100400    pathway3
Os01g0100466    pathway1
Os01g0100500    pathway9
Os01g0100600    pathway6
Os01g0100650    pathway78

can you please help?

ADD REPLY • link updated 2.5 years ago by GenoMax 148k • written 2.6 years ago by SKY ▴ 60

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You may need to add and configure database for the gene annotation, but you can try g:GOst from gProfiler suite of tools.

ADD REPLY • link 2.5 years ago by newbio17 ▴ 360

score 2 · Answer 1 · 2022-06-13

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2.5 years ago

Laura Luebbert ▴ 450

Try gget enrichr

ADD COMMENT • link 2.5 years ago by Laura Luebbert ▴ 450

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Can you show an example of how this tool can be used with the ID's posted above?

ADD REPLY • link 2.5 years ago by GenoMax 148k