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

[Steve Lianoglou]

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
...

I will look at this more closely later, though -- it looks very helpful.

Nice work!

-steve

-- 
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