Question: Different Results With Goose And Biomart
1
gravatar for TitoPullo
6.5 years ago by
TitoPullo150
United Kingdom
TitoPullo150 wrote:

I'm using the biomaRt package for R in order to get all the GO terms associated with with a particular Gene ID (Entrez ID). The script is quite simple and similar to the tutorial example:

ensembl = useMart("ensembl",dataset="hsapiens_gene_ensembl")
goids = getBM(attributes=c('entrezgene','go_id') ,filters='entrezgene', values=geneList, mart=ensembl)

This gives me a list of GO terms for each gene in geneList. In order to check these results I queried the GO dataset using GOOSE. So I translated Entrez ID into Uniprot ID and I executed a simple basic query (SQL Query by Uniprot ID). As result, usually the list obtained with biomaRt is longer than the one obtained using GOOSE (which directly query to GO dataset). How is this possible? Which method should I trust more? I think that GOOSE is more reliable, but why biomaRt list more GO terms?

R biomart go • 1.6k views
ADD COMMENTlink modified 6.5 years ago by secretjess170 • written 6.5 years ago by TitoPullo150

Can you please give an example?

ADD REPLYlink written 6.5 years ago by Bert Overduin3.6k
0
gravatar for secretjess
6.5 years ago by
secretjess170
Cambridge
secretjess170 wrote:

I'm wondering if it's something to do with the multiple products from a single gene or perhaps the mapping of GO terms to Entrez/Uniprot IDs? If you repeat your Ensembl query using "uniprot_swissprot" as your filter do you get the same result?

ADD COMMENTlink modified 6.5 years ago • written 6.5 years ago by secretjess170
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