Hi all, I am completely new in bioinformatics. I have a list containing about 8,000 fungi gene stable IDs and I am working in an experiment that requires me to map these gene stable IDs with any of Entrez ID, Ensembl ID or official symbol. Is there a website where I can copy and paste my fungi genes and it will return the result along with there Entrez ID, Ensembl ID or official symbols? I am just a newbie Thanks all
Hey Kris, I was able to use biomaRt (in R) to map these to RefSeq IDs and descriptive gene names. Does this work for you?
require(biomaRt) mart <- useMart(host="https://fungi.ensembl.org", biomart="fungi_mart", port = 443) mart <- useDataset("afumigatus_eg_gene", mart) afumigatus_ids <- c("AFUA_3G06200", "AFUA_3G06210", "AFUA_3G06230", "AFUA_3G06250") annotLookup <- getBM( mart = mart, attributes = c( "ensembl_gene_id", "refseq_peptide", "description"), filter = "ensembl_gene_id", values = afumigatus_ids, uniqueRows=TRUE) annotLookup ensembl_gene_id refseq_peptide 1 AFUA_3G06200 XP_754986.2 2 AFUA_3G06210 XP_754985.1 3 AFUA_3G06230 XP_754983.2 4 AFUA_3G06250 XP_754981.2 description 1 anaphase-promoting complex subunit Apc5, putative 2 phosphoribosyl-aminoimidazole-succinocarboxamide synthase 3 conserved hypothetical protein 4 RNA polymerase II mediator complex component Srb8, putative
You have to save your IDs in the vector called
biomaRt servers will not usually return the IDs in the same order as that in which they were submitted; so, be cautious of that.