Estimated colleagues,
I am working with CGH data. I have the name of the BAC clones and
their
chromosome locations. They correspond to OncoBAC arrays (?).
Is there any way in bioconductor to determine which genes belong to
each
BAC clone?
Thank you in advance,
Best,
Federico
PD: I am a newbie in R and Bioconductor
On Thursday 18 January 2007 11:32, Federico Abascal wrote:
> Estimated colleagues,
>
> I am working with CGH data. I have the name of the BAC clones and
their
> chromosome locations. They correspond to OncoBAC arrays (?).
> Is there any way in bioconductor to determine which genes belong to
each
> BAC clone?
I don't think there is a way directly in Bioconductor to do that.
However,
the UCSC table browser can "overlap" your BACs with other genome
annotation
such as genes. You might want to try there. They have a contact
email
address on their page and are quite helpful with queries like "how to
I
do...". Using their interface, you should have something
approximating what
you need in a few minutes.
Sean
Hi,
mapping BAC clones to genomic positions and genes can be a time
consuming process, especially if you have to do it manually. If
public
databases can help you depends on the way the BAC clones are named.
Could you give some example ?
Anyway, usually you should be able to get a table of BAC clones and
other parameters (genomic location, (uni)gene id etc.) which might
help
in identifiying the genes in question.
Regards, Hilmar
Federico Abascal schrieb:
> Estimated colleagues,
>
> I am working with CGH data. I have the name of the BAC clones and
their
> chromosome locations. They correspond to OncoBAC arrays (?).
> Is there any way in bioconductor to determine which genes belong to
each
> BAC clone?
>
> Thank you in advance,
> Best,
> Federico
>
>
> PD: I am a newbie in R and Bioconductor
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
http://news.gmane.org/gmane.science.biology.informatics.conductor
>
--
Hilmar Berger
Studienkoordinator
Institut f?r medizinische Informatik, Statistik und Epidemiologie
Universit?t Leipzig
H?rtelstr. 16-18
D-04107 Leipzig
Tel. +49 341 97 16 101
Fax. +49 341 97 16 109
email: hilmar.berger at imise.uni-leipzig.de
thank you very much for your responses Hilmar and Sean.
Hilmar Berger wrote:
> mapping BAC clones to genomic positions and genes can be a time
> consuming process, especially if you have to do it manually. If
public
> databases can help you depends on the way the BAC clones are named.
> Could you give some example ?
>
Here are some examples. I was unable to obtain information from the
UCSC
table browser (as Sean suggested), although I have to try it more.
CTD-2082H4
CTD-2060E7
RP11-130N6
RP11-142M16
RP11-221G13
RP11-238E12
CTD-2088A19
GS1-225F6
RP11-48J15
RP11-4D2
RP11-82L3
RP11-71M14
RP11-135H9
RP11-256K9
RP11-65G9
RP11-185N10
RP11-140H23
RP11-247J14
> Anyway, usually you should be able to get a table of BAC clones and
> other parameters (genomic location, (uni)gene id etc.) which might
help
> in identifiying the genes in question.
>
>
yes, I have that information.
Isn't there a way in Bioconductor to ask for the genes present between
nucleotides 130000 and 145000??
Best,
Federico
>> Estimated colleagues,
>>
>> I am working with CGH data. I have the name of the BAC clones and
their
>> chromosome locations. They correspond to OncoBAC arrays (?).
>> Is there any way in bioconductor to determine which genes belong to
each
>> BAC clone?
>>
Hi Federico,
Federico Abascal schrieb:
> CTD-2082H4
> CTD-2060E7
> RP11-130N6
> RP11-142M16
> RP11-221G13
> RP11-238E12
OK, these are standard BAC-Names you might find in public databases.
>
>>Anyway, usually you should be able to get a table of BAC clones and
>>other parameters (genomic location, (uni)gene id etc.) which might
help
>>in identifiying the genes in question.
>
> yes, I have that information.
> Isn't there a way in Bioconductor to ask for the genes present
between
> nucleotides 130000 and 145000??
Last time I had to map BAC clones to genes (actually to probesets) I
chose to use a list from GoldenPath (http://genome.ucsc.edu) because
that way it is easier to chose the release version of the genome
assembly. This release (or approximate date) should match the one that
was used for creation of your BAC-annotation list, since different
releases might have different positions for your BACs and genes.
The table "knownGene" from GoldenPath gives you start and end
positions
for each gene. A simple filter in R (e.g. "subset(gene.list,
gene.chrom=BAC.chrom & gene.start >= BAC.start & gene.stop <=
BAC.stop",
done for every BAC) should be sufficient to get all genes within or
nearby your BAC-clones.
Regards,
Hilmar
--
Hilmar Berger
Studienkoordinator
Institut f?r medizinische Informatik, Statistik und Epidemiologie
Universit?t Leipzig
H?rtelstr. 16-18
D-04107 Leipzig
Tel. +49 341 97 16 101
Fax. +49 341 97 16 109
email: hilmar.berger at imise.uni-leipzig.de
Giving you knew clone RP11-238E12 in ChrX, a straightforward
alternative might be to parse:
http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?taxid=9606&chr=X&maps=gen
es,clone[RP11-238E12]-r&cmd=txt
You can modify Build version as well.
Good luck!
Wenwu Cui, PhD
-----Original Message-----
From: Hilmar Berger [mailto:hilmar.berger@imise.uni-leipzig.de]
Sent: Friday, January 19, 2007 7:23 AM
To: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] from BAC name to list of genes in that BAC
Hi Federico,
Federico Abascal schrieb:
> CTD-2082H4
> CTD-2060E7
> RP11-130N6
> RP11-142M16
> RP11-221G13
> RP11-238E12
OK, these are standard BAC-Names you might find in public databases.
>
>>Anyway, usually you should be able to get a table of BAC clones and
>>other parameters (genomic location, (uni)gene id etc.) which might
help
>>in identifiying the genes in question.
>
> yes, I have that information.
> Isn't there a way in Bioconductor to ask for the genes present
between
> nucleotides 130000 and 145000??
Last time I had to map BAC clones to genes (actually to probesets) I
chose to use a list from GoldenPath (http://genome.ucsc.edu) because
that way it is easier to chose the release version of the genome
assembly. This release (or approximate date) should match the one that
was used for creation of your BAC-annotation list, since different
releases might have different positions for your BACs and genes.
The table "knownGene" from GoldenPath gives you start and end
positions
for each gene. A simple filter in R (e.g. "subset(gene.list,
gene.chrom=BAC.chrom & gene.start >= BAC.start & gene.stop <=
BAC.stop",
done for every BAC) should be sufficient to get all genes within or
nearby your BAC-clones.
Regards,
Hilmar
--
Hilmar Berger
Studienkoordinator
Institut f?r medizinische Informatik, Statistik und Epidemiologie
Universit?t Leipzig
H?rtelstr. 16-18
D-04107 Leipzig
Tel. +49 341 97 16 101
Fax. +49 341 97 16 109
email: hilmar.berger at imise.uni-leipzig.de
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