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Regarding cancer data analysis

Hi all,

I have a list of pathways and I want to know the genes that are involved in the particular pathway? For example, let's say vimentin, I wanted to know the list of approved genes in this particular pathway.

I will be glad if you help me

Thanks

rna-seq r gene genome
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updated by EagleEye EagleEye • written by selvasvce • selvasvce

What have you tried?

For example, let's say vimentin

What is vimentin? Is it a gene, protein, metabolite or drug? Please show us a little more effort to demonstrate you're invested in this.

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written by Ram Ram

Hi

it is a structural protein. Vimentin is a type III intermediate filament.

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written by selvasvce • selvasvce

I used Google to find what it is - that's not the point. You should add these details when you create the post. Also, you haven't answered my first question yet - what have you tried?

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written by Ram Ram

2 answers

Use Open targets database. Here is an example query with Vimentin.
Similar query at Reactome, Pathway commons.

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written by GenoMax GenoMax

Gene Set Clustering based on Functional annotation (GeneSCF)

With this tool you can retrieve all pathways with corresponding genes for your desired organism as simple text/table format. Example usage here

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written by EagleEye EagleEye

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