Question: Batch query obsolete gene names to get current HGNC symbol
1
gravatar for komal.rathi
2.8 years ago by
komal.rathi3.4k
Children's Hospital of Philadelphia, Philadelphia, PA
komal.rathi3.4k wrote:

Hi everyone,

I have a list of genes (n = 5726) for which I wanted to get the chrom, start and end. I used the following query:

library(biomaRt)
ensembl <- useMart("ensembl", dataset = "hsapiens_gene_ensembl")
lit.genes.ann <- getBM(attributes = c('chromosome_name','start_position','end_position','hgnc_symbol'), filters = 'hgnc_symbol', values = gene.names, mart = ensembl)

I got results for all but 79 genes back. This list was probably generated some time back and I am using the current ensembl build to get the data. I looked up one such gene EMR1 on Genecards and looks like it has been changed to ADGRE1.

Is there a way to do a batch search & import to get current HGNC symbols for all the obsolete genes that I have? I am not looking for all the aliases but just one approved HGNC symbol per obsolete gene name. Some of the gene names are:

ACN9
AQPEP
BAI1
PAPL
EMR1
ADD COMMENTlink modified 2.8 years ago • written 2.8 years ago by komal.rathi3.4k
3
gravatar for komal.rathi
2.8 years ago by
komal.rathi3.4k
Children's Hospital of Philadelphia, Philadelphia, PA
komal.rathi3.4k wrote:

Alright, I posted the question too soon I guess. For future reference - Multi-symbol checker worked.

ADD COMMENTlink written 2.8 years ago by komal.rathi3.4k
1

Great to see the OP reply in lightning speed answer to the question posted by self.

ADD REPLYlink modified 2.8 years ago • written 2.8 years ago by ivivek_ngs4.8k
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