Question

Enrichment Analysis with only GeneSymbols

0

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hamza_karakurt ▴ 60

@hamza_karakurt-17704

Last seen 2.4 years ago

Turkey

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 GSEA rna-seq scRna-Seq • 2.0k views

ADD COMMENT • link updated 5.8 years ago by Peter Langfelder ★ 3.0k • written 5.8 years ago by hamza_karakurt ▴ 60

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Hamza,

You could try the following code.

    library(ChIPpeakAnno)
    library(org.Hs.eg.db)
    enriched.GO = getEnrichedGO(listOfGeneSymbol, 
                                          orgAnn="org.Hs.eg.db", 
                                          maxP=0.1,
                                          minGOterm=10,
                                          feature_id_type = "gene_symbol",
                                          multiAdjMethod= "BH")
     dim(enriched.GO$mf)
     enriched.GO$mf
     enriched.GO$bp
     enriched.GO$cc

     library(reactome.db)
     enriched.PATH = getEnrichedPATH(listOfGeneSymbol, orgAnn="org.Hs.eg.db", 
                      pathAnn="reactome.db", maxP=0.1,
                       feature_id_type = "gene_symbol",
                      minPATHterm=10, multiAdjMethod="BH")
     library(KEGG.db)
     enriched.KEGG.PATH = getEnrichedPATH(listOfGeneSymbol, orgAnn="org.Hs.eg.db", 
                      pathAnn="KEGG.db", maxP=0.1,
                       feature_id_type = "gene_symbol",
                      minPATHterm=10, multiAdjMethod="BH")

For mouse, you need to change library(org.Hs.eg.db) to library(org.Mm.eg.db) and replace orgAnn = " org.Hs.eg.db".

Best regards,

Julie

ADD REPLY • link 5.8 years ago Julie Zhu ★ 4.3k

score 1 · Answer 1 · 2019-02-25

1

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James W. MacDonald 67k

@james-w-macdonald-5106

Last seen 11 hours ago

United States

In general all you need is a way to map the genes you measured to GO terms, for which a gene symbol can be useful. If the organism you are working with has relatively complete annotations there is probably an OrgDb package that you could use for that. But without more information that's about all anybody can tell you.

ADD COMMENT • link 5.8 years ago James W. MacDonald 67k

score 1 · Answer 2 · 2019-02-25

If standard gene sets like GO or KEGG is all you want, you could simply upload your genes to DAVID (https://david.ncifcrf.gov/). I believe DAVID will accept just gene symbols. I don't have a Bioconductor-only solution, but if you're willing to give it a try, anRichment (https://horvath.genetics.ucla.edu/html/CoexpressionNetwork/GeneAnnotation/, I am the principal author) would give you the functionality. The package has a fairly comprehensive tutorial, and the function to convert symbols to Entrez is convert2entrez. See the help page for the function once you install and load the package.