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I want to convert Ensembl ids to Gene_symbols. I used biomaRt package but all Ensembl ids are not seen in the results.

Examples of problematic IDs are: ENSG00000255414, ENSG00000274358, ENSG00000235565, ENSG00000278309. I gave them in bioDBnet, which seems to handle them.

I would like to know whether there is any R package for bioDBnet or not? If so, could you please tell how to use it?

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  • $\begingroup$ Welcome to Bioinformatics! This question seems to need more information to get a good answer. Could you please edit adding what is the G_list, and how did you create it? What do you mean by "I gave them in biodbnet"? Also some ensemble genes might not have an official name from the HGNC $\endgroup$
    – llrs
    Aug 27, 2017 at 11:59
  • $\begingroup$ Sorry. I edited the question now. Please check the link I gave !! $\endgroup$
    – stack_learner
    Aug 27, 2017 at 13:38
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    $\begingroup$ You might consider ignoring or removing those genes. The reason you dont find these genes are that they have been removed from the current data bases meaning the Ensembl people thinks it's a false postive (see ensembl.org/Homo_sapiens/Gene/Idhistory?g=ENSG00000255414 for example) $\endgroup$
    – Kristoffer Vitting-Seerup
    Aug 28, 2017 at 10:54
  • $\begingroup$ As @KristofferVitting-Seerup says, the real issue here is that you should not expect every ENSG to map to a HGNC symbol, for a variety of reasons. $\endgroup$
    – neilfws
    Aug 29, 2017 at 1:27
  • $\begingroup$ Ok. "gProfileR" is the best one for converting into gene_symbols and GO analysis too. There are no problematic IDs with that. Anyways thankyou all for the help. $\endgroup$
    – stack_learner
    Aug 29, 2017 at 8:06

2 Answers 2

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I couldn't find a package neither in Github nor in Bioconductor. Neither could I find any paper about a package linking to bioDBnet. So I don't believe there is any (R) package at the moment which links to biodbnet in order to retrieve the IDS.

However it has a couple of APIs so you could build one or use them to retrieve the information you want.

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  • $\begingroup$ I used "gProfileR". There are no problematic IDs with that. It converted ENSEMBL IDs to Gene_symbols and made my work easier with GO analysis too. There is an R package and also API. I recommend everyone to use this. Thank you all for the help !! $\endgroup$
    – stack_learner
    Aug 29, 2017 at 8:09
  • $\begingroup$ @user3351523 You are commenting to something different to what you asked. In this question you want to access to biodbnet, while in this comment you want to convert some IDs from ENSEMBL to Gene Symbols (Which can be done with several packages). $\endgroup$
    – llrs
    Aug 29, 2017 at 8:20
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library(EnsDb.Hsapiens.v86)
library(ensembldb)
genes(EnsDb.Hsapiens.v86)
genes(EnsDb.Hsapiens.v86, filter=GeneIdFilter('ENSG00000235857'))
transcripts(EnsDb.Hsapiens.v86, filter = GeneIdFilter("ENSG00000184895"),
              order.by = "tx_seq_start")

(The ids you listed are older than v86). See the vignette for the ensembldb Bioconductor package.

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    $\begingroup$ Although helpful, I think it won't help the original poster (and other readers) if you do not explain how did you identify that the ids provided were older than a specific version. Also explaining that this package is able to convert these ids would help to the original poster $\endgroup$
    – llrs
    Jan 9, 2019 at 11:41

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