Abdul Rawoof | 28 Jun 06:57 2013
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Re: Regarding extraction of 3' and 5'UTRs and exonic region of a gene.

Thanks for your kind suggestion and I will try to follow your suggested
workflow and obviously it will take time to learn all this packages as I
never go through it.

One more thing I want to ask that how can I download the list of all
available cancer genes for human from Kegg database  for wnt signaling
pathways??
Please forgive me if I asked any senseless question as I have not tried
that mentioned packages till now.

Thanks,
Abdul Rawoof

On Thu, Jun 27, 2013 at 11:01 PM, Hervé Pagès <hpages@...> wrote:

> Hi Abdul,
>
> Suggested workflow:
>
> 1. Build the list of genes involved in the particular cancer you're
>    interested in. Could be a vector of gene ids or transcript ids (not
>    all transcripts are necessarily linked to a gene).
>
>    Suggested tools (no exhaustive): GO.db and org.Hs.eg.db packages,
>    maybe the DO.db package, etc... I'm not sure what would be the best
>    tool for this. But maybe you already have your list of genes?
>
> 2. Use the TxDb.Hsapiens.UCSC.hg19.**knownGene + GenomicFeatures packages
>    to extract the coordinates of the 5'UTRs and 3'UTRs.
>    Use the fiveUTRsByTranscript() and threeUTRsByTranscript() functions
>    for this. They'll return the result in a GRangesList object (you'll
>    have to become a bit familiar with those objects first).
>
> 3. Use the BSgenome.Hsapiens.UCSC.hg19 package and the
>    extractTranscriptsFromGenome() function from the GenomicFeatures
>    package to extract the UTR sequences.
>    The name of the function is misleading but it can be used to extract
>    CDS or UTR sequences in addition to transcript sequences.
>
> If you've never used those tools before, it will take you some time to
> get familiarized with them. Your best friends are the man pages for the
> individual functions/classes you're going to run into (don't miss the
> examples section) and the vignettes in the GenomicRanges and
> GenomicFeatures package.
>
> Let us know if you have specific questions or run into specific problems
> (show us what you've done and explain the problem -- don't forget your
> sessionInfo()).
>
> Good luck,
> H.
>
>
> On 06/27/2013 01:58 AM, Abdul Rawoof wrote:
>
>> Hello everyone,
>>
>>
>> Could anyone show me the way how can I extract the *3' and 5' UTRs and
>> exonic regions *of all *Human genes* from *Ensembl and Kegg database* that
>> are involved in particular cancer specially *breast cancer *using
>>
>> R/Biocondutor.
>>
>> Thanks in advance.
>>
>> Abdul Rawoof
>>
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>>
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>>
> --
> Hervé Pagès
>
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
>
> E-mail: hpages@...
> Phone:  (206) 667-5791
> Fax:    (206) 667-1319
>

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