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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