I used the “Analyse gene expression” tool with my mouse proteomics data set. I notice that the database is based on human pathways – does the software automatically convert my mouse gene names to the human orthologs? Or can’t I use the software for mouse?

Reactome’s manual curation covers human proteins, but we do support analysis of non-human data sets.

There are two methods to analyze data in Reactome. 

The “Analyse gene list” tool, accessed after “Analysis” is selected from the home page,  allows users to upload human or non-human data sets for overrepresentation analysis. After uploading the data with this tool, the user is given the option of ‘projecting to human’ (which is selected by default). If this toggle is selected, non-human identifiers in the data set are converted to their human equivalents using orthology information from Panther. 

Data sets can also be analyzed with the Reactome Gene Set Analysis (Reactome GSA) tool, accessed through the “Analyze Gene Expression” button after “Analysis” is selected from the home page.  Reactome GSA performs quantitative pathway analyses, increasing the statistical power of the differential gene expression analysis. The analysis software automatically converts the mouse proteins from your proteomics set to their human orthologs.