Selecting MOUSE gene set libraries in Enrichr

Question

[Jen]

I see there are currently 212 gene set libraries available in Enrichr (https://maayanlab.cloud/Enrichr/index.jsp#). I am running Enrichr on the web and not in R. In scrolling through the 212 gene set libraries, I see there are mouse libraries available (i.e. KEGG_2019_Mouse) but the algorithm does not seem to run against them and only returns results for human (i.e. KEGG_2021_Human). It also does not let you select which library you'd like to use. Because there are mouse gene set libraries available here, I assume there is a way to select them but I cannot seem to figure out how. Nor can I figure it out in R. Can someone please tell me if this is even possible? If not, I will quit wasting my time.

Answer 1

[fracarb8]

On the website, you cannot select which database to use, but they released an updated tool (Enrichr-KG) which seems to allows you to do so.

In R, you can easily achieve that with

library(enrichR)
# get list of all available libraries
dbs <- listEnrichrDbs()  

# make a selection of libraries to use 
dbs_selection <- c("Mouse_Gene_Atlas","KEGG_2019_Mouse",...)
# to get all the databased for mouse
dbs_selection <- unique(dbs$libraryName)[grep("Mouse",unique(dbs$libraryName))]

mouse_genes <- c("Runx1", "Gfi1", "Gfi1b", "Spi1", "Gata1", "Kdr")
enriched <- enrichr(mouse_genes, dbs_selection)

[Jen]

Thank you for your comment. I initially was using the web interface because I was having trouble inputing a background list of genes using R. The Enrichr manual says that I can do this using the background argument. I tried the following:

KEGG2019 <- c("KEGG_2019_Mouse")
mouse_genes <- read.table("3383CCGs.txt")
background <- read.table("Background list of enpressed genes 13569.txt")
enriched <- enrichr(mouse_genes, KEGG2019, background=background)

Error in enrichr(mouse_genes, KEGG2019, background = background) :    unused argument (background = background)

I don't suppose you have any wisdom as to the correct way to input the background argument here?? Nothing helpful is coming up in my searching.

[fracarb8]

Where did you read that it accepts background genes? The R implementation is a wrapper around the website (it sends the data over their servers), and does not accept a background argument. Have a look at their repo