Question: Enrichment Analysis with only GeneSymbols
0
gravatar for hamza_karakurt
4 months ago by
hamza_karakurt30 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 gsea scrna-seq • 144 views
ADD COMMENTlink modified 4 months ago by Peter Langfelder2.1k • written 4 months ago by hamza_karakurt30
1

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 REPLYlink modified 4 months ago • written 4 months ago by Julie Zhu4.0k
Answer: Enrichment Analysis with only GeneSymbols
1
gravatar for James W. MacDonald
4 months ago by
United States
James W. MacDonald50k wrote:

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 COMMENTlink written 4 months ago by James W. MacDonald50k
Answer: Enrichment Analysis with only GeneSymbols
1
gravatar for Peter Langfelder
4 months ago by
United States
Peter Langfelder2.1k wrote:

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.

ADD COMMENTlink modified 4 months ago • written 4 months ago by Peter Langfelder2.1k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 297 users visited in the last hour