Last week I extracted the 3UTR sequences for a list of genes identified through their Entrez_num. The biologist we are working with is not happy yet ... and asked me to provide the following: Regarding the 3'UTR database I need for now the following: 1) UTR sequence 2) name of the gene 3) where the 3'UTR is located in the gene sequence. In other terms the coordinates of where 3'UTR starts and ends. Thanks I thought it would be an easy task but I incurred in the following error: > genes_map <- getBM(attributes=c("entrezgene","hgnc_symbol","ensembl_ gene_id","ensembl_transcript_id","3_utr_start","3_utr_end"), + filters = "entrezgene", values=genes.ds[1:3,1], mart=hmart) Error in getBM(attributes = c("entrezgene", "hgnc_symbol", "ensembl_gene_id", : Query ERROR: caught BioMart::Exception::Usage: Attributes from multiple attribute pages are not allowed I cannot see what I am doing wrong. Your help is very welcome. Thank you in advance. Maura tutti i telefonini TIM! [[alternative HTML version deleted]]

Hi Maura, mauede at alice.it wrote: > Last week I extracted the 3UTR sequences for a list of genes identified through their Entrez_num. > The biologist we are working with is not happy yet ... and asked me to provide the following: > > Regarding the 3'UTR database I need for now the following: > > 1) UTR sequence > 2) name of the gene > 3) where the 3'UTR is located in the gene sequence. In other terms the coordinates of where 3'UTR starts and ends. > Thanks > > I thought it would be an easy task but I incurred in the following error: >> genes_map <- getBM(attributes=c("entrezgene","hgnc_symbol","ensembl _gene_id","ensembl_transcript_id","3_utr_start","3_utr_end"), > + filters = "entrezgene", values=genes.ds[1:3,1], mart=hmart) > Error in getBM(attributes = c("entrezgene", "hgnc_symbol", "ensembl_gene_id", : > Query ERROR: caught BioMart::Exception::Usage: Attributes from multiple attribute pages are not allowed This has to do with the way the Biomart webserver/database is set up. Essentially, you can't do gene-based queries and transcript-based queries at one time. But you can do them sequentially and merge at the end. > mart <- useMart("ensembl","hsapiens_gene_ensembl") Checking attributes ... ok Checking filters ... ok > suppressMessages(library(org.Hs.eg.db)) > egs <- head(Lkeys(org.Hs.egSYMBOL)) ## just getting some IDs > egs [1] "1" "10" "100" "1000" "10000" "100008586" > a <- getBM(c("entrezgene","hgnc_symbol","ensembl_gene_id", "ensembl_transcript_id"), "entrezgene", egs, mart) > head(a) entrezgene hgnc_symbol ensembl_gene_id ensembl_transcript_id 1 1 A1BG ENSG00000121410 ENST00000263100 2 10 NAT2 ENSG00000156006 ENST00000286479 3 100 ADA ENSG00000196839 ENST00000372874 4 1000 CDH2 ENSG00000170558 ENST00000269141 5 10000 AKT3 ENSG00000117020 ENST00000366539 6 10000 AKT3 ENSG00000117020 ENST00000366540 > b <- getBM(c("ensembl_transcript_id", "3_utr_start","3_utr_end"), "ensembl_transcript_id", as.character(a[,4]), mart) > head(b) ensembl_transcript_id 3_utr_start 3_utr_end 1 ENST00000263100 NA NA 2 ENST00000263100 58858172 58858387 3 ENST00000263826 NA NA 4 ENST00000263826 243666484 243668550 5 ENST00000269141 NA NA 6 ENST00000269141 25530930 25532116 > d <- merge(a,b) > head(d) ensembl_transcript_id entrezgene hgnc_symbol ensembl_gene_id 3_utr_start 1 ENST00000263100 1 A1BG ENSG00000121410 NA 2 ENST00000263100 1 A1BG ENSG00000121410 58858172 3 ENST00000263826 10000 AKT3 ENSG00000117020 NA 4 ENST00000263826 10000 AKT3 ENSG00000117020 243666484 5 ENST00000269141 1000 CDH2 ENSG00000170558 25530930 6 ENST00000269141 1000 CDH2 ENSG00000170558 NA 3_utr_end 1 NA 2 58858387 3 NA 4 243668550 5 25532116 6 NA Best, Jim > > I cannot see what I am doing wrong. > Your help is very welcome. > > Thank you in advance. > Maura > > > tutti i telefonini TIM! > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues