Hi Matthias,
You can get Ensembl gene IDs directly in one query. If you need gene name you
may do something like this:
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE Query>
<Query virtualSchemaName = "default" formatter = "TSV" header = "0" uniqueRows
= "0" count = "" datasetConfigVersion = "0.6" >
<Dataset name = "hsapiens_snp" interface = "default" >
<Filter name = "refsnp" value = "rs4399482,rs12885778"/>
<Attribute name = "refsnp_id" />
<Attribute name = "chr_name" />
<Attribute name = "chrom_start" />
<Attribute name = "ensembl_gene_stable_id" />
<Attribute name = "ensembl_transcript_stable_id" />
</Dataset>
<Dataset name = "hsapiens_gene_ensembl" interface = "default" >
<Attribute name = "external_gene_id" />
</Dataset>
</Query>
Cheers,
Jana (Ensembl helpdesk)
On 14 Mar 2011, at 18:38, Matthias Macé wrote:
> Elena,
> OK, that's what I thought : it seems impossible to directly retrieve the
> result. So why is there the 'start-end' SNP option ? It seems useless, isn't
> it ?
> I hoped to perform this task in one "shot" since I plan to do this on more
> than 30 000 queries.
> I hope I do not bother you with my (stupid) questions...
> Many thanks,
> Matthias
>
> Al 14/03/2011 19:19, En/na Elena Rivkin ha escrit:
>>
>> Matthias,
>> I used your SNPs in 'Ensembl variation' and I got the following
>> coordinates (see attached.
>>
>> rs12885778 (chr 14) 20404091
>> rs4399482 (chr 14) 20137587
>>
>> XML query:
>> <?xml version="1.0" encoding="UTF-8"?>
>> <!DOCTYPE Query>
>> <Query virtualSchemaName = "default" formatter = "TSV" header = "0"
>> uniqueRows = "0" count = "" datasetConfigVersion = "0.6" >
>>
>> <Dataset name = "hsapiens_snp" interface = "default" >
>> <Filter name = "refsnp" value = "rs4399482,rs12885778"/>
>> <Attribute name = "refsnp_id" />
>> <Attribute name = "chr_name" />
>> <Attribute name = "chrom_start" />
>> </Dataset>
>> </Query>
>>
>>
>> Entering these bp into gene search I got 10 genes (see attached).
>>
>> XML query:
>> <?xml version="1.0" encoding="UTF-8"?>
>> <!DOCTYPE Query>
>> <Query virtualSchemaName = "default" formatter = "TSV" header = "0"
>> uniqueRows = "0" count = "" datasetConfigVersion = "0.6" >
>>
>> <Dataset name = "hsapiens_gene_ensembl" interface = "default" >
>> <Filter name = "chromosome_name" value = "14"/>
>> <Filter name = "end" value = "20404091"/>
>> <Filter name = "start" value = "20137587"/>
>> <Attribute name = "ensembl_gene_id" />
>> <Attribute name = "ensembl_transcript_id" />
>> </Dataset>
>> </Query>
>>
>>
>>
>> Elena
>>
>>
>>
>>
>> On 11-03-14 2:08 PM, "Matthías Macé" <[email protected]> wrote:
>>
>>> Elena,
>>> FIrst, thank you for your valuable help.
>>> I tried your method (using rs4399482 <-> rs12885778). By querying UCSC,
>>> they return "OR11H2,OR4K1,OR4K2,OR4K5,OR4M1,OR4N2,OR4Q3".
>>> However, when I try with Biomart, I get an empty field (with either
>>> ENsembl ID or HGNC). I queried dbSNP and for the first SNP, it told me
>>> that it was an Illumina SNP. I replaced with the corresponding dbSNP ID
>>> once more, it failed.
>>> Any idea ?
>>> Best regards,
>>> Matthias
>>>
>>> Al 14/03/2011 17:03, En/na Elena Rivkin ha escrit:
>>>> Matthias,
>>>> Just to add to Arek's suggestion you can also try using the 'Marker'
>>>> filters in the REGION section.
>>>> If this does not work, SNPs can be converted to their genomic
>>>> coordinates (this can be done using Ensembl variation datasets), and
>>>> then these coordinates can be used to identify the genes.
>>>>
>>>> Elena
>>>>
>>>> From: Arek Kasprzyk
>>>> <[email protected]<mailto:[email protected]>>
>>>> Date: Mon, 14 Mar 2011 11:45:52 -0400
>>>> To: "[email protected]<mailto:[email protected]>"
>>>> <[email protected]<mailto:[email protected]>>,
>>>> "[email protected]<mailto:[email protected]>"
>>>> <[email protected]<mailto:[email protected]>>
>>>> Cc: "[email protected]<mailto:[email protected]>"
>>>> <[email protected]<mailto:[email protected]>>
>>>> Subject: Re: [BioMart Users] Biomart xml query
>>>>
>>>> Ok, I got it.
>>>> Perhaps multiple genomic region filter could the the trick. Input
>>>> coordinate segments there and output the genes
>>>>
>>>> Try Ensembl 61, Home sapiens genes, 'REGION' section, "multpile
>>>> chromosomal regions". See if this helps
>>>>
>>>>
>>>>
>>>> a
>>>>
>>>> Arek Kasprzyk
>>>> Director, Bioinformatics Operations and Principal Investigator
>>>>
>>>> Ontario Institute for Cancer Research
>>>> MaRS Centre, South Tower
>>>> 101 College Street, Suite 800
>>>> Toronto, Ontario, Canada M5G 0A3
>>>>
>>>> Tel: 416-673-8559
>>>> Toll-free: 1-866-678-6427
>>>> www.oicr.on.ca
>>>>
>>>> Administrative Assistant:
>>>> [email protected]<mailto:[email protected]>
>>>>
>>>> This message and any attachments may contain confidential and/or
>>>> privileged information for the sole use of the intended recipient. Any
>>>> review or distribution by anyone other than the person for whom it was
>>>> originally intended is strictly prohibited. If you have received this
>>>> message in error, please contact the sender and delete all copies.
>>>> Opinions, conclusions or other information contained in this message may
>>>> not be that of the organization.
>>>>
>>>> From: Matthias Macé
>>>> <[email protected]<mailto:[email protected]>>
>>>> Reply-To: "[email protected]<mailto:[email protected]>"
>>>> <[email protected]<mailto:[email protected]>>,
>>>> "[email protected]<mailto:[email protected]>"
>>>> <[email protected]<mailto:[email protected]>>
>>>> Date: Mon, 14 Mar 2011 11:40:10 -0400
>>>> To: Arek Kasprzyk
>>>> <[email protected]<mailto:[email protected]>>
>>>> Subject: Re: [BioMart Users] Biomart xml query
>>>>
>>>> Hi Arek,
>>>> No, I give the following input :
>>>> rsID_1
>>>> rs_ID_2
>>>>
>>>> and i wish to retrieve a list of genes at least overlapping with the
>>>> segment "rs_ID_1<-->rs_ID_2".
>>>>
>>>> query: rs_ID_1---------------------------rs_ID_2
>>>> <-----------gene_1------------->
>>>> <-------gene_2--------->
>>>>
>>>> <-----------gene_3------------->
>>>>
>>>> It would return : gene_1, gene_2, gene_3
>>>>
>>>> Thanks,
>>>> Matthias
>>>>
>>>>
>>>>
>>>> Al 14/03/2011 16:30, En/na Arek Kasprzyk ha escrit:
>>>>
>>>> Hi MM,
>>>> Are you asking for the SNP/gene consequences such as 'non_synonymous',
>>>> 'intronic' etc?
>>>>
>>>>
>>>> a
>>>> Arek Kasprzyk
>>>> Director, Bioinformatics Operations and Principal Investigator
>>>>
>>>> Ontario Institute for Cancer Research
>>>> MaRS Centre, South Tower
>>>> 101 College Street, Suite 800
>>>> Toronto, Ontario, Canada M5G 0A3
>>>>
>>>> Tel: 416-673-8559
>>>> Toll-free: 1-866-678-6427
>>>> www.oicr.on.ca<http://www.oicr.on.ca>
>>>>
>>>> Administrative Assistant:
>>>> [email protected]<mailto:[email protected]>
>>>>
>>>> This message and any attachments may contain confidential and/or
>>>> privileged information for the sole use of the intended recipient. Any
>>>> review or distribution by anyone other than the person for whom it was
>>>> originally intended is strictly prohibited. If you have received this
>>>> message in error, please contact the sender and delete all copies.
>>>> Opinions, conclusions or other information contained in this message may
>>>> not be that of the organization.
>>>>
>>>> From: Matthias Macé
>>>> <[email protected]<mailto:[email protected]><mailto:matthias.
>>>> [email protected]><mailto:[email protected]>>
>>>> Reply-To:
>>>> "[email protected]<mailto:[email protected]><mailto:matthias.
>>>> [email protected]><mailto:[email protected]>"
>>>> <[email protected]<mailto:[email protected]><mailto:matthias.
>>>> [email protected]><mailto:[email protected]>>,
>>>> "[email protected]<mailto:[email protected]><mailto:matthias.
>>>> [email protected]><mailto:[email protected]>"
>>>> <[email protected]<mailto:[email protected]><mailto:matthias.
>>>> [email protected]><mailto:[email protected]>>
>>>> Date: Mon, 14 Mar 2011 11:22:30 -0400
>>>> To: Arek Kasprzyk
>>>> <[email protected]<mailto:[email protected]><mailto:arek.ka
>>>> [email protected]><mailto:[email protected]>>
>>>> Subject: Re: [BioMart Users] Biomart xml query
>>>>
>>>> Dear Arek,
>>>> Many thanks for your quick answer !
>>>> However, I already did what you tlod me on a previous query, but now,
>>>> my problem is that I cannot find the mapping I told you on the web-based
>>>> interface (i.e. snp segment >> overlapping genes). I can only retrieve
>>>> annotation for every snp.
>>>> Isn't there any way to perform "segment-query" ?
>>>> Cheers,
>>>> MM
>>>>
>>>>
>>>> Al 14/03/2011 15:57, En/na Arek Kasprzyk ha escrit:
>>>>
>>>> Director, Bioinformatics Operations and Principal Investigator
>>>>
>>>> --
>>>> "Only two things are infinite, the universe and human stupidity, and
>>>> I'm not sure about the former." -Albert Einstein
>>>> Dr Matthias Macé, DVM, PhD
>>>> INSERM U1043
>>>> C.H.U. Purpan - BP 3028
>>>> 31024 TOULOUSE CEDEX 3
>>>> tel: (33) 562 74 45 09
>>>> mobile: (33) 608 881481
>>>> http://www.u563.toulouse.inserm.fr/
>>>>
>>>>
>>>> --
>>>> "Only two things are infinite, the universe and human stupidity, and
>>>> I'm not sure about the former." -Albert Einstein
>>>> Dr Matthias Macé, DVM, PhD
>>>> INSERM U1043
>>>> C.H.U. Purpan - BP 3028
>>>> 31024 TOULOUSE CEDEX 3
>>>> tel: (33) 562 74 45 09
>>>> mobile: (33) 608 881481
>>>> http://www.u563.toulouse.inserm.fr/
>>>>
>>> --
>>> "Only two things are infinite, the universe and human stupidity, and I'm
>>> not sure about the former." -Albert Einstein
>>> --
>>> "[...] si un jour nos villes et nos campagnes sont enfin libérées de
>>> cette détestable présence exotique [les immigrés], eh bien, ce jour-là,
>>> c¹est simplement que ce seront les chers enfants de Lille, de Nantes, de
>>> Sheffield ou de Birmingham qui prendront leur baluchon, feront leurs
>>> adieux et partiront vivre, travailler, aimer et mourir ailleurs."
>>> [http://bloginlondon.wordpress.com/2010/01/29/les-anglais-decouvrent-les-c
>>> harmes-du-lepenisme/]
>>>
>>
>
>
> --
> "Only two things are infinite, the universe and human stupidity, and I'm not
> sure about the former." -Albert Einstein
> Dr Matthias Macé, DVM, PhD
> INSERM U1043
> C.H.U. Purpan - BP 3028
> 31024 TOULOUSE CEDEX 3
> tel: (33) 562 74 45 09
> mobile: (33) 608 881481
> http://www.u563.toulouse.inserm.fr/
> _______________________________________________
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> https://lists.biomart.org/mailman/listinfo/users
Jana Vandrovcova, Ph.D.
User Support Officer
EMBL - European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton, Cambridge CB10 1SD
United Kingdom
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