Map genes to the ids

Question

[liftedkris4all]

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

[Prakash]

Have you looked into fungiDB ?

[liftedkris4all]

Thanks this is a great suggestion but it doesn’t have the exact symbols i want

[Kevin Blighe]

It may help to paste a sample of the IDs that you have.

[Liftedkris]

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

AFUA_3G06190
AFUA_3G06200
AFUA_3G06210
AFUA_3G06230
AFUA_3G06250
AFUA_3G06255
AFUA_3G06260
AFUA_3G06270
AFUA_3G06280
AFUA_3G06290
AFUA_3G06300
AFUA_3G06310
AFUA_3G06320
AFUA_3G06330
AFUA_3G06340
AFUA_3G06350
AFUA_3G06360
AFUA_3G06370

[mks002]

You can try out g:Profiler. Hope this would solve your query.

[Liftedkris]

thanks for your response and suggestion, however this did not accept my ids. here is a sample

AFUA_3G06190
AFUA_3G06200
AFUA_3G06210
AFUA_3G06230
AFUA_3G06250
AFUA_3G06255
AFUA_3G06260
AFUA_3G06270
AFUA_3G06280
AFUA_3G06290
AFUA_3G06300
AFUA_3G06310
AFUA_3G06320
AFUA_3G06330
AFUA_3G06340
AFUA_3G06350
AFUA_3G06360
AFUA_3G06370

[dsull]

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

Answer 1

[Kevin Blighe]

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.

[Liftedkris]

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?

[jared.andrews07]

You can read in your IDs directly from a file, you don't have to enter them manually.

[17th Level Botanist]

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")