Bioinformatics Asked by gabt on June 7, 2021
Lets say I performed a single cell RNA sequencing analysis on mice blood samples. Eventually I am able to cluster cells together and get a set of genes of interest for each cell type since I want to study the gene expression of specific cells after a treatment.
At this point I want to perform an enrichment analysis to get a list of those GO biological processes and/or molecular functions that might be affected by the novel genes that are up or down regulated after the treatment. I can use several tools such as ClusterProfiler, Panther, EnrichR but, and this is the point, should I use gene sets that are compiled for mouse only or can I enrich my genes using gene sets compiled from other organisms too such as, for instance, human gene sets? Is it ok to mix genes and gene sets from different organisms when performing an enrichment?
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