Pathway Enrichment

Question

[SKY]

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!

[Hamid Ghaedi]

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.

[SKY]

thank you. will try and get back.

[ATpoint]

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?

[SKY]

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?

[newbio17]

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

Answer 1

[Laura Luebbert]

Try gget enrichr

[GenoMax]

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