[BioC] Agilent annotation source

[Sean Davis]

On Thu, Feb 4, 2010 at 9:29 AM, James W. MacDonald
<jmacdon at med.umich.edu> wrote:
> Hi Axel,
>
> axel.klenk at actelion.com wrote:
>>
>> Dear BioC list and Biocore Data Team,
>>
>> we are using various Agilent arrays and the recent paper by Gertz et al.
>> ( http://www.biomedcentral.com/1471-2164/10/566 ) made me feel a
>> little bit uneasy about the annotation provided by that vendor.
>>
>> As far as I understand, BioC annotation, e.g. in package hgug4112a.db,
>> is using EntrezGene IDs as keys to retrieve public annotation for a given
>> EntrezGene entry -- but where does the mapping from Agilent's Oligo ID
>> to EntrezGene come from?
>
> The first mapping is usually vendor --> Entrez Gene using the manufacturer's
> annotation data. However, in this case, it appears that the mapping was
> vendor --> GenBank and then all other mappings were from GenBank. From
> ?hgug4112aACCNUM:
>
> For chip packages such as this, the ACCNUM mapping comes directly from the
> manufacturer. This
> is different from other mappings which are mapped onto the probes via an
> Entrez Gene identifier.
>
>>
>> I have tried to find the answer in the package's reference manual and help
>> pages but would prefer to be absolutely sure in this case...
>>
>> Thanks in advance,
>>  - axel
>>
>>
>> P.S., I do not yet have much experience with sequence analysis in BioC
>> and would also be grateful for pointers to packages that could help me
>> verify oligo mappings myself.
>
> There may be more recent examples of how to do this, but the GenomeSearching
> vignette:
>
> http://bioconductor.org/packages/2.5/bioc/vignettes/BSgenome/inst/doc/GenomeSearching.pdf
>
> has a good example in section 8. You can then use the output from that
> alignment with e.g. rtracklayer to visualize, or the org.Xx.eg.db package to
> map to genes.

I'll just add a bit to Jim's suggestions.  For the 50-60mers on the
Agilent array, one probably wants to map to a transcript database and
NOT the genome, as many of these probes will cross exon boundaries.  A
program like blat or gmap (or bioconductor tools) can align the
agilent probes to a trancript database such as RefSeq or Ensembl known
transcripts.  In the end, alignment to transcripts is what is
typically sought, anyway, for gene expression arrays.

Sean

>>
>>
>> Axel Klenk
>> Research Informatician
>> Actelion Pharmaceuticals Ltd / Gewerbestrasse 16 / CH-4123 Allschwil /
>> Switzerland
>>
>>
>>
>>
>> The information of this email and in any file transmitted with it is
>> strictly confidential and may be legally privileged.
>> It is intended solely for the addressee. If you are not the intended
>> recipient, any copying, distribution or any other use of this email is
>> prohibited and may be unlawful. In such case, you should please notify the
>> sender immediately and destroy this email.
>> The content of this email is not legally binding unless confirmed by
>> letter.
>> Any views expressed in this message are those of the individual sender,
>> except where the message states otherwise and the sender is authorised to
>> state them to be the views of the sender's company. For further information
>> about Actelion please see our website at http://www.actelion.com
>>
>> _______________________________________________
>> 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
>
> --
> James W. MacDonald, M.S.
> Biostatistician
> Douglas Lab
> University of Michigan
> Department of Human Genetics
> 5912 Buhl
> 1241 E. Catherine St.
> Ann Arbor MI 48109-5618
> 734-615-7826
> **********************************************************
> Electronic Mail is not secure, may not be read every day, and should not be
> used for urgent or sensitive issues
> _______________________________________________
> 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
>