help) can't find hgnc_symbol

[Donghee Lee]

Hi groups,

I want to convert ENSG to HGNC symbol, so I ran biomaRt as follows:

##

library("biomaRt")

ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl")

test1 <- getBM(attributes = c('ensembl_gene_id', 'hgnc_symbol'),

                          filters = 'ensembl_gene_id',

                          values = test$Gene_symbol,

                          mart = ensembl)

but there are some ENSGs remained unchanged.

215	ENSG00000197406	DIO3
216	ENSG00000197714	ZNF460
217	ENSG00000197943
218	ENSG00000198467	TPM2
219	ENSG00000198496	NBR2
220	ENSG00000198919	DZIP3

I can figure out what the ENSG is... in ensembl web browser.

Gene: PLCG2 (ENSG00000197943) - Summary - Homo sapiens ...

https://www.ensembl.org › ENSG00000197943

이 페이지 번역하기

Gene: PLCG2 ENSG00000197943 . Description. phospholipase C gamma 2 [Source:NCBI gene;Acc:5336]. Gene Synonyms. APLAID, FCAS3, PLC-IV, ...

Can I try something?

Thanks,

Best,

Donghee

[Thomas Maurel]

Dear Donghee,
It’s true that most Gene names are coming from HGNC for human. In some cases, we have Ensembl genes that are not mapped to any HGNC data so we select another external reference as the Gene name. For example the gene name PLCG2 for ENSG00000197943 is coming from NCBI gene as you can see on this page: https://www.ensembl.org/Homo_sapiens/Gene/Matches?g=ENSG00000197943;r=16:81739097-81962685.

If you are only interested in HGNC symbols then your query is correct and ENSG00000197943 is not mapped to any HGNC data.

If you are interested in Gene Names, you can use the Gene name and source attributes as below:

> library("biomaRt")

> ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl")

> 

> test1 <- getBM(attributes = c('ensembl_gene_id', 'external_gene_name','external_gene_source'),

+                filters = 'ensembl_gene_id',

+                values = "ENSG00000197943",

+                mart = ensembl)

> test1

  ensembl_gene_id external_gene_name external_gene_source

1 ENSG00000197943              PLCG2            NCBI gene

Hope this helps,

Kind Regards,

Thomas 

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Thomas Maurel
Bioinformatician - Ensembl Production Team
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
United Kingdom

[Donghee Lee]

Dear Thomas

Thank you very much. It helped a lot!!

Best,

Donghee

2019년 8월 30일 금요일 오후 9시 8분 47초 UTC+9, Thomas Maurel 님의 말:

Dear Donghee,
It’s true that most Gene names are coming from HGNC for human. In some cases, we have Ensembl genes that are not mapped to any HGNC data so we select another external reference as the Gene name. For example the gene name PLCG2 for ENSG00000197943 is coming from NCBI gene as you can see on this page: https://www.ensembl.org/Homo_sapiens/Gene/Matches?g=ENSG00000197943;r=16:81739097-81962685.

If you are only interested in HGNC symbols then your query is correct and ENSG00000197943 is not mapped to any HGNC data.

If you are interested in Gene Names, you can use the Gene name and source attributes as below:

> library("biomaRt")

> ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl")

> 

> test1 <- getBM(attributes = c('ensembl_gene_id', 'external_gene_name','external_gene_source'),

+                filters = 'ensembl_gene_id',

+                values = "ENSG00000197943",

+                mart = ensembl)

> test1

  ensembl_gene_id external_gene_name external_gene_source

1 ENSG00000197943              PLCG2            NCBI gene

Hope this helps,

Kind Regards,

Thomas 

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