Question: Enrichment Analysis with only GeneSymbols
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gravatar for hkarakurt
6 months ago by
hkarakurt80
hkarakurt80 wrote:

Hello everyone, I was looking to other posts but could not find a proper answer. I have a list of significantly changed genes and I want to do enrichment analysis with them. Is there a R/Bioconductor package that does this analysis with only GeneSymbols. Most of the packages require other informations or transcription data. I used EnrichR but since it does not have an option for organism, I have some human pathways as answer for mouse genes. I just want to do a hypergeometric test to identify enriched terms like in the http://geneontology.org

Thank you in advance.

R rna-seq enrichment scrna-seq • 218 views
ADD COMMENTlink modified 6 months ago by caggtaagtat760 • written 6 months ago by hkarakurt80
1

David may be useful for you, easy and fast, I does not require a rank table (Fold, pvalue etc.)

ADD REPLYlink modified 6 months ago • written 6 months ago by Buffo1.7k

I am looking for a R/Bioconductor package in fact but DAVID looks really nice also.

Thank you.

ADD REPLYlink written 6 months ago by hkarakurt80
0
gravatar for caggtaagtat
6 months ago by
caggtaagtat760
caggtaagtat760 wrote:

I just used Agrigo, which is also suiteable for human an mouse genes. You have to convert the gene IDs to MGI IDs though, for example with the help of the biomart of ensembl. It than gives you the GO-terms plus the p-value for their enrichment test.

This table can then be used for condensing the information with REVIGO.

ADD COMMENTlink written 6 months ago by caggtaagtat760
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