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Annotating gene function categorisation in r

Hi

I have generated a list of filtered gene symbol ids. However I would now like to list the functional category of each gene.

So my current gene list looks like

IDH1
IDH2
AKT1
ATM
ATP50
NCOR
ABC

I would like to be able to convert this into something along the lines of:

GeneSymbol       Category
IDH1                      Cell Cycle
IDH2                      Apoptosis
AKT1                     Cellular signalling

Is there a tool in r that can do this?

gene r
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updated by Ram Ram • written by The_PyPanda • The_PyPanda

1 answer

See https://reactome.org/download-data and use the Reactome Pathways Gene Set. You can easily read that into R with fgsea::fgsea::gmtPathways(). Then simply intersect the genes with this resource. Note that for many genes there is not a single but many intersecting terms.

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written by ATpoint ATpoint

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