yxngl
commented
1 year ago Hi, MsigDB Hallmarks is just for human. You could potentially map your genes to human orthologs and use it. But whether it is appropriate is up to you. I would just do pathway enrichment first in mouse and it shouldn't miss out too much. But it could be a supplementary result as well.
On Tue, Aug 16, 2022 at 12:59 PM bryanrhelm @.***> wrote:
Hello, I am doing functional enrichment with some up- and downregulated gene lists, and I'm getting an error when I try to use the community contributed hallmarks of cancer database. Here is my code:
c0vs1.up.hallmarks <- WebGestaltR(enrichMethod = "ORA", organism = "mmusculus", enrichDatabase = "community-contributed_Hallmark50", interestGene = rownames(degs.0vs1.up), interestGeneType = "genesymbol", referenceSet = "genome", isOutput = F, minNum = 5)
This error is produced when I run the code: "Loading the functional categories... ERROR: Please select the functional database or select 'others' to upload the functional database.Error in loadGeneSet(organism = organism, enrichDatabase = enrichDatabase, : ERROR: Please select the functional database or select 'others' to upload the functional database."
- I can get an output if I change the organism to "hsapiens" and convert the mouse gene symbols to human by converting to uppercase.
I was wondering if there is a way to use the mouse gene symbols directly to perform functional enrichment for the MsigDB Hallmarks database or is it appropriate to convert to human symbols for the enrichment?
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Hello, I am doing functional enrichment with some up- and downregulated gene lists, and I'm getting an error when I try to use the community contributed hallmarks of cancer database. Here is my code:
c0vs1.up.hallmarks <- WebGestaltR(enrichMethod = "ORA", organism = "mmusculus", enrichDatabase = "community-contributed_Hallmark50", interestGene = rownames(degs.0vs1.up), interestGeneType = "genesymbol", referenceSet = "genome", isOutput = F, minNum = 5)
This error is produced when I run the code: "Loading the functional categories... ERROR: Please select the functional database or select 'others' to upload the functional database.Error in loadGeneSet(organism = organism, enrichDatabase = enrichDatabase, : ERROR: Please select the functional database or select 'others' to upload the functional database."
I was wondering if there is a way to use the mouse gene symbols directly to perform functional enrichment for the MsigDB Hallmarks database or is it appropriate to convert to human symbols for the enrichment?