Question

how can I annotate some of my genes

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Bioinformatics ▴ 30

@bioinformatics-10931

Last seen 2.8 years ago

United States

I have a serious problem with gene ID annotation :-)

I am converting the ensemble_ID to gene names

this is an example of IDs

ENSG00000122718 ENSG00000130201 ENSG00000150076 ENSG00000150526 ENSG00000155640 ENSG00000166748 ENSG00000168260 ENSG00000168787 ENSG00000170590 ENSG00000170803 ENSG00000171484 ENSG00000172381 ENSG00000172774

here is what I do

data = read.table("list_ensembl_gid.tsv") colnames(data)[1] <- "ensembl_gene_id" colnames(data)[2] <- "counts" library('biomaRt') hsapiens = useMart("ensembl", dataset="hsapiens_gene_ensembl") hsapiens_infos <- getBM(attributes=c('ensembl_gene_id', 'external_gene_name'), mart = hsapiens) merge_infos <- merge(x = data, y = hsapiens_infos, by = "ensembl_gene_id", all.x = TRUE)

biomart r • 936 views

ADD COMMENT • link updated 6.8 years ago by Mike Smith ★ 6.6k • written 6.8 years ago by Bioinformatics ▴ 30

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What exactly is the problem? You're using a number of packages and functions here, but haven't said what is going wrong, or what output you're currently generating.

ADD REPLY • link 6.8 years ago Mike Smith ★ 6.6k

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@Mike Smith I dont have any problem with programing. The problem is that I cannot annotate them to gene name. Aparently these are old biomart database. Is there any possibility to annotate them ? can you please just run and see it by yourself?

ADD REPLY • link 6.8 years ago Bioinformatics ▴ 30

score 0 · Answer 1 · 2018-01-22

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Mike Smith ★ 6.6k

@mike-smith

Last seen 5 minutes ago

EMBL Heidelberg

These IDs are no longer in the Ensembl database e.g. ENSG00000155640

Gene: ENSG00000155640

This identifier is not in the current EnsEMBL database

You can use an old version of Ensembl, but your probably better off working out why you're getting these out-of-date gene IDs in your results. To use the old Ensembl archive you can do:

hsapiens = useMart("ensembl",
                   dataset="hsapiens_gene_ensembl",
                   host = "http://sep2015.archive.ensembl.org")

ADD COMMENT • link 6.8 years ago Mike Smith ★ 6.6k

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@Mike Smith the problem is that the data is coming from TCGA and they were aligned in 2014-2015. They don't release teh raw files and I should use the htseq-count as it is. I am having issue with about 3000 genes which are outdated. I dont want to discard them but also I did not know how to get them assigned to a gene name. I will see if I can get them annotaed

ADD REPLY • link 6.8 years ago Bioinformatics ▴ 30