Using available reference set in WebGestaltR
Entering edit mode
9 weeks ago
mzuer • 0

Dear All,

Using the WebGestaltR R package I would like to do an enrichment analysis with a list of genes (see at the bottom), using the full set of human genes as reference.

I was not able to find what is the geneType that should be used for the sets provided by WebGestaltR (i.e. those listed with listReferenceSet()) (I wanted to use "genome")

Also, do you know where I can find more information about the gene types of the reference sets (and other infos) that are provided ?

I tried the following (and several other things...), but it did not work:

enrichResult <- WebGestaltR(enrichMethod="ORA", organism="hsapiens", enrichDatabase="pathway_KEGG", interestGene=my_genes, interestGeneType="genesymbol", referenceGene="genome", referenceGeneType="genesymbol", isOutput=F)

with my_genes being

my_genes [1] "WDR68" "BOP1" "RAE1" "NUP85" "CDC123" "HSF1" "KARS" "E2F4"
[9] "OGFOD1" "RPL8" "FAM96B" "AARS" "NUP93" "CSNK2A2" "COQ9" "DDX19A" [17] "IQCK" "MRPL12" "DDX19B" "NIP7" "FBXO7" "JMJD6" "STAM" "ANKRD11" [25] "CIAPIN1" "CIRH1A" "ZNF319" "PDSS1" "DDB1" "DYNLL2" "CCNE1" "DUS2L"
[33] "KATNB1" "MASTL" "KLHL36" "CP110" "RFWD3" "DPH2" "CHMP6" "SF3B3" [41] "WDR45L" "PSMD7" "WRNIP1" "SNRPB" "PSMC3IP" "HMBS" "MFN1" "MLX"
[49] "SIRT7" "COX4NB" "PRR11" "RAD51AP1" "USP10" "HEATR3" "AURKA" "CMAS"

gsea webgestaltr gene_enrichment • 80 views

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