[biomart-users] help) can't find hgnc_symbol

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

Can I try something?

Thanks,

Best,
Donghee

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Re: [biomart-users] help) can't find hgnc_symbol

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 

On 25 Aug 2019, at 16:10, Donghee Lee <[hidden email]> wrote:

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.

215ENSG00000197406DIO3
216ENSG00000197714ZNF460
217ENSG00000197943
218ENSG00000198467TPM2
219ENSG00000198496NBR2
220ENSG00000198919DZIP3

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

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

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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

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Re: [biomart-users] help) can't find hgnc_symbol

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: <a href="https://www.ensembl.org/Homo_sapiens/Gene/Matches?g=ENSG00000197943;r=16:81739097-81962685" target="_blank" rel="nofollow" onmousedown="this.href=&#39;https://www.google.com/url?q\x3dhttps%3A%2F%2Fwww.ensembl.org%2FHomo_sapiens%2FGene%2FMatches%3Fg%3DENSG00000197943%3Br%3D16%3A81739097-81962685\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNEDODlufc1bFFDQB8cU4q5ek9RZJQ&#39;;return true;" onclick="this.href=&#39;https://www.google.com/url?q\x3dhttps%3A%2F%2Fwww.ensembl.org%2FHomo_sapiens%2FGene%2FMatches%3Fg%3DENSG00000197943%3Br%3D16%3A81739097-81962685\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNEDODlufc1bFFDQB8cU4q5ek9RZJQ&#39;;return true;">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 

On 25 Aug 2019, at 16:10, Donghee Lee <<a href="javascript:" target="_blank" gdf-obfuscated-mailto="HeYzTdCrAQAJ" rel="nofollow" onmousedown="this.href=&#39;javascript:&#39;;return true;" onclick="this.href=&#39;javascript:&#39;;return true;">nerd....@...> wrote:

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.

215ENSG00000197406DIO3
216ENSG00000197714ZNF460
217ENSG00000197943
218ENSG00000198467TPM2
219ENSG00000198496NBR2
220ENSG00000198919DZIP3

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

<a href="https://www.ensembl.org/id/ENSG00000197943" rel="nofollow" style="color:rgb(102,0,153)" target="_blank" onmousedown="this.href=&#39;https://www.google.com/url?q\x3dhttps%3A%2F%2Fwww.ensembl.org%2Fid%2FENSG00000197943\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNHHvPacluPYxkiXv31KwVyy6xiqSQ&#39;;return true;" onclick="this.href=&#39;https://www.google.com/url?q\x3dhttps%3A%2F%2Fwww.ensembl.org%2Fid%2FENSG00000197943\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNHHvPacluPYxkiXv31KwVyy6xiqSQ&#39;;return true;">

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


https://www.ensembl.org › ENSG00000197943
<a href="https://www.google.com/search?q=ENSG00000197943&amp;oq=ENSG00000197943&amp;aqs=chrome..69i57.837j0j7&amp;sourceid=chrome&amp;ie=UTF-8#" style="border-top-left-radius:0px;border-top-right-radius:0px;border-bottom-right-radius:0px;border-bottom-left-radius:0px;font-size:11px;font-weight:bold;min-height:12px;line-height:27px;margin-top:1px;margin-bottom:2px;min-width:0px;text-align:center;background-image:none;color:rgb(68,68,68);width:13px;display:inline-block" target="_blank" rel="nofollow" onmousedown="this.href=&#39;https://www.google.com/search?q\x3dENSG00000197943\x26oq\x3dENSG00000197943\x26aqs\x3dchrome..69i57.837j0j7\x26sourceid\x3dchrome\x26ie\x3dUTF-8#&#39;;return true;" onclick="this.href=&#39;https://www.google.com/search?q\x3dENSG00000197943\x26oq\x3dENSG00000197943\x26aqs\x3dchrome..69i57.837j0j7\x26sourceid\x3dchrome\x26ie\x3dUTF-8#&#39;;return true;">
  1. <a href="https://webcache.googleusercontent.com/search?q=cache:6pq9Lp4HAOsJ:https://www.ensembl.org/id/ENSG00000197943+&amp;cd=1&amp;hl=ko&amp;ct=clnk&amp;gl=kr" rel="nofollow" style="color:rgb(51,51,51);font-size:16px;display:block;padding:7px 18px;outline:0px" target="_blank" onmousedown="this.href=&#39;https://webcache.googleusercontent.com/search?q\x3dcache:6pq9Lp4HAOsJ:https://www.ensembl.org/id/ENSG00000197943+\x26cd\x3d1\x26hl\x3dko\x26ct\x3dclnk\x26gl\x3dkr&#39;;return true;" onclick="this.href=&#39;https://webcache.googleusercontent.com/search?q\x3dcache:6pq9Lp4HAOsJ:https://www.ensembl.org/id/ENSG00000197943+\x26cd\x3d1\x26hl\x3dko\x26ct\x3dclnk\x26gl\x3dkr&#39;;return true;">
<a href="https://translate.google.com/translate?hl=ko&amp;sl=en&amp;u=https://www.ensembl.org/id/ENSG00000197943&amp;prev=search" rel="nofollow" style="color:rgb(26,13,171);font-size:16px" target="_blank" onmousedown="this.href=&#39;https://translate.google.com/translate?hl\x3dko\x26sl\x3den\x26u\x3dhttps://www.ensembl.org/id/ENSG00000197943\x26prev\x3dsearch&#39;;return true;" onclick="this.href=&#39;https://translate.google.com/translate?hl\x3dko\x26sl\x3den\x26u\x3dhttps://www.ensembl.org/id/ENSG00000197943\x26prev\x3dsearch&#39;;return true;">이 페이지 번역하기
Gene: PLCG2 ENSG00000197943 . Description. phospholipase C gamma 2 [Source:NCBI gene;Acc:5336]. Gene Synonyms. APLAID, FCAS3, PLC-IV, ...
<a href="https://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000197943" rel="nofollow" style="color:rgb(102,0,153)" target="_blank" onmousedown="this.href=&#39;https://www.google.com/url?q\x3dhttps%3A%2F%2Fgrch37.ensembl.org%2FHomo_sapiens%2FGene%2FSummary%3Fdb%3Dcore%3Bg%3DENSG00000197943\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNETCugGy55Jk2WM6fmnHG4al4N6BA&#39;;return true;" onclick="this.href=&#39;https://www.google.com/url?q\x3dhttps%3A%2F%2Fgrch37.ensembl.org%2FHomo_sapiens%2FGene%2FSummary%3Fdb%3Dcore%3Bg%3DENSG00000197943\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNETCugGy55Jk2WM6fmnHG4al4N6BA&#39;;return true;">

Can I try something?

Thanks,

Best,
Donghee

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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

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