Question: Correlation matrix between enhancers and promoters (human)?
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gravatar for daniele.avancini
7 weeks ago by
daniele.avancini10 wrote:

Dear all, I need your help in finding a file I downloaded while ago but I cannot find anymore online. The file is a correlation matrix between enhancer and promoters calculated as described in An atlas of active enhancers across human cell types and tissues (Andersson et al, 2014).

The file is composed by: - the genomic coordinates of the enhancer - the associated promoter (gene) - the distance between enhancer-promoter, - correlation value - FDR value.

Can you help me in finding it? Thanks in advance for the time spent reading this stupid query.

ADD COMMENTlink modified 7 weeks ago • written 7 weeks ago by daniele.avancini10

Perhaps it's in the supplementary information?

Supplementary figure 25 for example has a heatmap showing cell type by enhancers.

ADD REPLYlink written 7 weeks ago by manuel.belmadani570
1
gravatar for daniele.avancini
7 weeks ago by
daniele.avancini10 wrote:

I've spoken directly to the curators of the FANTOM5 database and they directed me to the source of the file. To whom it may concern, this is the link to enhancer-promoter correlation matrix I was talking about:

http://slidebase.binf.ku.dk/human_enhancers/presets

Section number 5 contains the matrices.

ADD COMMENTlink written 7 weeks ago by daniele.avancini10
1
gravatar for geek_y
7 weeks ago by
geek_y9.3k
Barcelona/CRG/London/Imperial
geek_y9.3k wrote:

Enhancer promoter correlations are tricky because they are highly cell-type specific. Make sure the dataset you are using actually used cell-type or tissue-type of your interest in their correlation analysis. For example, if you are working with liver and the correlations are calculated without including liver data, you should be cautious to use those correlations.

Also check data from Reconstruction of enhancer–target networks in 935 samples of human primary cells, tissues and cell lines

ADD COMMENTlink written 7 weeks ago by geek_y9.3k

Thanks, @geek_y. That was one of the paper I took information from but it wasn't the source of my file.

ADD REPLYlink written 7 weeks ago by daniele.avancini10
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