Question: Suggested tools for enhancer
gravatar for steffanchristiansen
2.9 years ago by
University of Copenhagen
steffanchristiansen0 wrote:

Dear all

I am going to investigate enhancers in human heart tissue. Currently, I am using the VISTA Enhancer Browser to search for enhancers, but I am a little conserned due to lack of consensus of the suggested enhancer locations by the browser and displayed VISTA enhancers by UCSC Genome Browser. The elements do not overlap even though the data should be derived from the same studies and I use the hg19 genome for both browsers.

Have anybody faced similar problems? Alternatively, does anyone suggest other browsers/tools for finding location of enhancers regulating specific genes?

ADD COMMENTlink modified 2.9 years ago • written 2.9 years ago by steffanchristiansen0

Can you give an example?

ADD REPLYlink written 2.9 years ago by ATpoint38k

I have uploaded this screenshot of the enhancer called element_1978. When I use the Vista Enhancer Browser, it maps the element to that specific position. However according to the UCSC browser, there is no element at that position.

ADD REPLYlink modified 2.9 years ago • written 2.9 years ago by steffanchristiansen0

The enhancer you refer to is classified as negative. I assume that the track only includes such called positive, e.g. chr16:86,430,087-86,430,726). Still, this database you are using only contains about 2500 enhancers, because it requires extensive in vivo confirmation, therefore excluding like 99.9% of NGS-identified enhancers (ChIP/ATAC/STARR/CAGE-seq). Still, each cell type contains thousands of enhancer elements, so I am not really sure if using this database is the best choice, but this of course depends on your scientific question. What exactly is your task?

ADD REPLYlink written 2.9 years ago by ATpoint38k

Good to know! Expected that all enhancers (whether they are positive or not) would be included.

My task is to investigate regulation of heart specific genes in human heart tissue. I selected that database because I had an assumption that the in vivo confirmed enhancers were more likely to reflect the regulation in human tissue compared to predicted enhancers for instance. My analysis are based on a targeted approach and therefore, I need to limit my investigation to few regions with a (presumably) higher probability of observing gene regulation.

ADD REPLYlink written 2.9 years ago by steffanchristiansen0
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