Hi All, I am new in the field of pathway analysis. I am trying to use the ReactomeGSA package on a single cell RNA-seq dataset from mouse. The package works well and there's the possibility to investigate the pathways on the Reactome website (https://reactome.org/content/query?q=R-HSA-1059683&species=Mus+musculus&species=Homo+sapiens&cluster=true)

ReactomeGSA package can be used to get pathway-level expression values for every cell cluster. This is achieved by calculating the mean gene expression for every cluster and then submitting this data to a gene set variation analysis. All of this is wrapped in the single analyse_sc_clusters function that I used on my Seurat T cells subset: gsvaresult <- analysescclusters(Tcells, verbose = TRUE)

After running the analyse_sc_clusters function, I run the pathways function that returns the pathway-level expression values per cell cluster: pathwayexpression <- pathways(gsvaresult)

The problem is that the result gives me only human pathways IDs e.gR-HSA-1059683).

Did anyone use this package on other non-human species?

Thank you very much

Hi,

Short answer: Unfortunately, there is no way to retrieve mouse pathway ids.

Long answer: Reactome is a manually curated pathway database. The curation is done only for human pathways. All other species are then automatically derived from the source human data by mapping the respective identifiers. With very few exceptions, there are no real mouse specific curated pathways.

In order to support multi-species pathway comparisons, we only return the human pathways in ReactomeGSA. As this is the original data in Reactome, you will not loose any biological information.

Does that help!

Kind regards, Johannes