Annotating gene function categorisation in r

Question

[The_PyPanda]

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?

[zx8754]

Read about biomaRt: https://cran.r-project.org/web/packages/biomartr/vignettes/Functional_Annotation.html

Answer 1

[ATpoint]

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.