Question: Enrichment Analysis with only GeneSymbols
0
gravatar for hkarakurt
17 months ago by
hkarakurt100
hkarakurt100 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 • 372 views
ADD COMMENTlink modified 17 months ago by caggtaagtat1.1k • written 17 months ago by hkarakurt100
1

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

ADD REPLYlink modified 17 months ago • written 17 months ago by Buffo1.8k

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

Thank you.

ADD REPLYlink written 17 months ago by hkarakurt100
0
gravatar for caggtaagtat
17 months ago by
caggtaagtat1.1k
caggtaagtat1.1k 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 17 months ago by caggtaagtat1.1k
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