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I have a list of cell markers differentially expressed between 2 groups of cells, that I got with the FindMarkers command in Seurat. I want to enrich for those genes that are expressed in the cell membrane. Are there any specific tools/commands I can use to do that? Thanks!

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  • $\begingroup$ Could you explain what do you mean by "enrich" test if some group is differently expressed or retrieve more information about those genes from other sources? $\endgroup$ – llrs Jun 3 '19 at 8:32
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You can do functional enrichment analysis, for instance with gProfiler in R and see if your marker genes are enriched in any GO term related with the plasma membrane.

Alternatively, you can generate a list with genes whose product are located at the plasma membrane and perform Gene Set Enrichment Analysis, for instance with fgsea in R.

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