Hi all,

I am recently looking into the DNase data of ENCODE project. For one celline, I think the DNaseI HS Peaks from ENCODE/Duke is the right one I am looking for.

However, there are two kinds of such data,
1) DNaseI HS Peaks from ENCODE/Duke

2) DNaseI HS Uniform Peaks from ENCODE/Analysis

So what's the difference of these two types of data, I can not find anywhere for description.

Another question is that cellines may be processed with some treatment, so what's the difference between with and without such treatment?

Hope to get answers.

Thanks

Yes, I know it is a kind of meta-analysis, but it do not have the p-value, and the counts for the DHSs regions of uniform are more than the idividual one

The p-values (FDR) that they used are listed in the link I gave you. You should have access to all the info.

chr1 10100 10250 . 0 . 5 -1 -1 -1 chr1 237740 237890 . 0 . 12 -1 -1 -1 chr1 565400 565550 . 0 . 39 -1 -1 -1 chr1 565840 565990 . 0 . 62 -1 -1 -1 chr1 566720 566870 . 0 . 60 -1 -1 -1 chr1 566980 567130 . 0 . 38 -1 -1 -1 chr1 567560 567710 . 0 . 75 -1 -1 -1 chr1 569780 569930 . 0 . 9279 -1 -1 -1

I paste the part of file here, please take a look at the last three coloms, which should be: pValue -1 float range Statistical significance of signal value (-log10). Set to -1 if not used. qValue -1 float range Statistical significance with multiple-test correction applied (FDR -log10). Set to -1 if not used. peak -1 int(11) range Point-source called for this peak; 0-based offset from chromStart. Set to -1 if no point-source called.

As you can see, all the last three colums are set to -1, which means they do not do any significant test?

The content is taken from file : HUVEC DNase HUVEC DNaseI HS Uniform Peaks from ENCODE/Analysis

I guess they did statistical tests but did not report the values unfortunately. That's bad but you can try to email them. I am not at all related to ENCODE so I do not know more.

Great thanks, I believe so since I guess these uniform peaks should be more condident ones while it seems that all of this kind of data do not provide p-value

Anyway, thanks, I will email to them for answer.