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:[email protected]><mailto:[email protected]>> > Reply-To: > "[email protected]<mailto:[email protected]><mailto:[email protected]><mailto:[email protected]>" > > <[email protected]<mailto:[email protected]><mailto:[email protected]><mailto:[email protected]>>, > > "[email protected]<mailto:[email protected]><mailto:[email protected]><mailto:[email protected]>" > > <[email protected]<mailto:[email protected]><mailto:[email protected]><mailto:[email protected]>> > Date: Mon, 14 Mar 2011 11:22:30 -0400 > To: Arek Kasprzyk > <[email protected]<mailto:[email protected]><mailto:[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, c’est 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-charmes-du-lepenisme/]
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