Question: Identify trans-regulatory regions
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gravatar for carlosalfonsogonzalez6
3.1 years ago by
carlosalfonsogonzalez610 wrote:

Hello everyone

I was wondering, Which are the current methods to identify trans-regulatory modules? I have seen in recent articles, the use of hybrids where the expression of the parental lines is compared with the heterozygotes of F1 through RNA-seq, although this method is able to identify the genes that are differentially regulated, does not say much about the regulatory regions that contribute to the differential expression, What methods would you suggest to find these regulatory modules that occur in trans?

ADD COMMENTlink modified 3.1 years ago by jared.andrews078.3k • written 3.1 years ago by carlosalfonsogonzalez610
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gravatar for Hussain Ather
3.1 years ago by
Hussain Ather940
National Institutes of Health, Bethesda, MD
Hussain Ather940 wrote:

Clustering and linkage analysis has been used https://www.nature.com/articles/ng1222

ADD COMMENTlink written 3.1 years ago by Hussain Ather940
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gravatar for jared.andrews07
3.1 years ago by
jared.andrews078.3k
Memphis, TN
jared.andrews078.3k wrote:

Trans regulation is a difficult thing to pin down, though one of the more high throughput methods is to utilize Hi-C to find interchromosomal/long-distance DNA interactions. Of course, this doesn't help pin down more convoluted trans regulation (ie. by your differentially expressed lncRNAs or transcription factors), but it's one of the more straightforward genome-wide analyses you can do if you're not trying to determine the regulation of specific loci.

ADD COMMENTlink written 3.1 years ago by jared.andrews078.3k
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gravatar for carlosalfonsogonzalez6
3.1 years ago by
carlosalfonsogonzalez610 wrote:

i didnt see this method as a solution, i think they take too many asumptions, clustering gene expresión seems like an easy path, What do you think?

ADD COMMENTlink written 3.1 years ago by carlosalfonsogonzalez610

Welcome to biostars! This isn't an answer - if you want to comment on somebody's answer, add a comment to it (as I'm doing now). This helps keep the question organized and makes discussions easier to follow.

ADD REPLYlink written 3.1 years ago by jared.andrews078.3k
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