Mapping Mouse RNAseq Marker Genes to Reactome Pathways

Question

[el24]

Hello,

In my project, I need to correlate single-cell RNAseq marker genes (after clustering) with specific pathways, for example metabolism and the immune system in Mus musculus. Here is what my marker genes look like:

       Gene   logFC   adj.P.Val
 1     gene1   -0.09   3e-06
 2     gene2   1.3     2-05
 3     gene3   1.5     1e-05

While I have found resources for Homo sapiens, I'm struggling to locate equivalent data (tabular format) for Mus musculus in Reactome that shows pathways and associated genes. My objective is to determine the overlap of my RNAseq marker genes with these mouse pathways.

I have seen this tutorial to do so on human data analysis, but now I need to find pathways and their related genes for mouse data. I'm working with single-cell gene expression files, doing pre-processing, clustering, and marker gene analysis using Scanpy, much like the Seurat standard pipeline.

Could anyone guide me on how to effectively extract Mus musculus pathways and associated gene information from Reactome or suggest alternative resources for this analysis?

Thank you very much in advance.

Answer 1

[NancyTLi]

Reactome has equivalent pathways for non-human species such as mouse from orthoinference with Panther DB. I am not sure what format you are looking for, but if you download the Reactome pathways you will see the non-human species are included in many of the files: https://reactome.org/download-data