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/] >
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