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 afumigatus_ids.
biomaRt servers will not usually return the IDs in the same order as that in which they were submitted; so, be cautious of that.
thanks so much this is fantastic! but now i have almost 9000 of the genes, how do i handle it because it is too much to be entered manually?
You can read in your IDs directly from a file, you don't have to enter them manually.
To read your gene names in from a file, you just need to modify Kevin's code from
afumigatus_ids <- c("AFUA_3G06200", "AFUA_3G06210", "AFUA_3G06230", "AFUA_3G06250")
to
afumigatus_ids <- readLines("your.file")
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Have you looked into fungiDB ?
Thanks this is a great suggestion but it doesn’t have the exact symbols i want
It may help to paste a sample of the IDs that you have.
thanks so much for efforts to assist me. what i have is a bunch of around 9000 fungi gene stable IDs. here is a sample
You can try out g:Profiler. Hope this would solve your query.
thanks for your response and suggestion, however this did not accept my ids. here is a sample
biomaRt works great as previously suggested. Here's another tool that I often find useful for converting between gene symbols, IDs, etc.: https://biodbnet-abcc.ncifcrf.gov/db/db2db.php