[Bioc-devel] ¿A useful addition to MotifDb package?

Steve Lianoglou mailinglist.honeypot at gmail.com
Thu Oct 11 20:25:00 CEST 2012


On Wed, Oct 10, 2012 at 2:56 PM, Hervé Pagès <hpages at fhcrc.org> wrote:
> Hi Steve, Paul,
> On 10/09/2012 09:03 AM, Steve Lianoglou wrote:
>> Hi Paul,
>> On Tue, Oct 9, 2012 at 11:29 AM, Paul Shannon <pshannon at fhcrc.org> wrote:
>>> Hi Steve,
>>> Very timely, very helpful!   Just yesterday I proposed to Martin, as a
>>> taks for the coming sprint:
>>>   4) Add the new TF PWMs from ENCODE into MotifDb
>>> I had not yet gotten as far as locating the data at ebi.  Thanks!
>>> If you care to take a look, perhaps comment, this Bioc workflow became
>>> visible yesterday, but has not yet been generally announced:
>>>    http://www.bioconductor.org/help/workflows/gene-regulation-tfbs/
>> Interesting.
>> I'll have to take a closer look at it later. I (really) quickly
>> skimmed the first 1/4th of it -- here is a rather minor comment:
>> Under the "Sequence Search" section, the numbers for "loosely"
>> defining the promoter bounds is 1k-3k up and 100-300 downstream from
>> the TSS. I think these numbers aren't too controversial if you're
>> talking about yeast (which the workflow seems to be about), but it
>> might not hurt to specify that these numbers may not be appropriate in
>> all contexts -- as another point of ref, the paper I linked to uses 5k
>> up/down stream from the TSS for "proximal regulatory regions" of genes
> So I wonder if it would not be better to not provide default values
> for the 'upstream' and 'downstream' arguments of the promoters()
> extractor. Whatever we do, getPromoterSeq() and promoters() should
> probably do the same (default values of 2000 and 200 for promoters(),
> no default values for getPromoterSeq()).

I'm +0 on not including default values, but whatever the decision is,
agree w/ you that getPromoterSeq() and promoters() should have the
same defaults (I actually never knew these functions existed ;-)

Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact

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