[Genome] A question about regulatory potential scores (regPotential7X.txt for mouse)

[Kayla Smith]

Shan,

I suggest contacting the scientists who created this data, listed on the
details page for this track
(http://genome.ucsc.edu/cgi-bin/hgTrackUi?g=regPotential7X) to learn more
about exactly how the items in the table are partitioned up into regions.

Since you are looking for precise scores, one thing to keep in mind when
looking at this data is that it is in compressed form and so may appear
incorrect in some cases.

Here is a link to the uncompressed wiggle values for this data:
http://www.bx.psu.edu/~james/esperr_rp_7way_scores/genome_scores_mm8/chr1.scores.truncated.bz2

I hope this is helpful to you.  Please don't hesitate to contact us
again if you require further assistance.

Kayla Smith
UCSC Genome Bioinformatics Group



Kayla Smith
UCSC Genome Bioinformatics Group

On Mon, 2 Jul 2007, Shan Yang wrote:

> Hi,
>
> I just downloaded the "regPotential7X.txt" file for mm8. Here is a
> question I have about the data.
> For example, the 1st line in the file says:
>
> 608     chr1    3050242 3050650
> chr1.0  1       408     0       /gbdb/mm8/wib/regPotential7X.wib
>    0       0.144514        408     1.67677 0.187318
>
> To my understanding, this basically means that the 408 bp long region
> has a min score of 0 and max score of 0.144514 and the sum of score
> in this region is 1.67677, which makes the average to be 0.00408028.
> According to the description of this score, anything over 0.001 may
> have a big potential to be a regulatory element, which means this
> regions is highly possible to be a regulatory element. But if I look
> at the browser, I can see that the main contributor of this average
> score in this 408bp region is a subregion of chr1:3050626-3050650
> (25bp). So does this mean that this subregion has more potential than
> any other nt in this region or every nt in this entire 408 bp region
> has the same potential? I think the first should be right. If this is
> true, then why does the file record the whole 408 region rather than
> just the subregion?
>
> Thanks a lot!
>
> Shan
>
>
> Shan Yang, PhD
> Genome Biology Division, L-452
> Chemistry,  Materials & Life Sciences Directorate (CMLS)
> Lawrence Livermore National Laboratory
> 7000 East Ave, Livermore, CA, 94550
>
> Ph:  925-422-7389
> Fax: 925-422-2099
> _______________________________________________
> Genome maillist  -  Genome at soe.ucsc.edu
> http://www.soe.ucsc.edu/mailman/listinfo/genome
>