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Enhancer Identification for Specific Genes

enhancers epigenetics bioinformatics histones

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#1 SarahLee8

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Posted 17 December 2015 - 11:14 AM

Hello all,

 

I had this in a different sub-forum, but I decided that it would better apply to this forum.

 

My lab is investigating human gene expression and epigenetics. My specific project that I'm getting started on now is focusing on enhancers.  One component of the project is looking at changes in the enrichment of histone modifications that are characteristic of enhancers (i.e. H3K27ac, H3K4me1/2, etc...) in response to a specific treatment.  We have data already that the modifications do significantly change in response to our experimental treatments (we used high resolution mass spec for that).  We also have a separate data set from an expression microarray that shows genes that have increased/decreased expression in response to our treatment.  To pick up from here, I want to first hand-pick some candidate genes from the microarray data to run qPCRs and I'm most interested in genes that are known to have associated enhancers in the literature and hopefully some extensive ENCODE data from other cell lines.  

 

So finally on to my specific question: what is the best way to go about mining all the literature and data out there to find the information that I want?  Honestly, I'm a little overwhelmed by the massive amount of information collected as part of ENCODE.  I've tried playing around with the tracks within the UCSC genome browser, but I have no idea what is the most efficient way to do this.  I'd like to narrow down by defined enhancers and the enhancer histone PTMs and be able to specifically search the most significantly changed genes in my lab's microarray data (ChIP-seq data, I guess?).

 

I appreciate any guidance that all of you amazing scientists can provide!

 

Best,

 

SarahLee



#2 bob1

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Posted 17 December 2015 - 12:10 PM

Probably not the news you wanted to hear, but usually if there isn't an answer, its because no-one knows the answer.

 

Have you looked at the software tools page, there is a link there for tools that you might find interesting/useful for mining the data.



#3 SarahLee8

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Posted 04 January 2016 - 10:06 AM

Thank you very much for your response!

 

I had a feeling that was the reason for the lack of response.  I know the users on this site are very vigilant and helpful whenever possible.

 

I have explored that tools page, but it is probably worth a little more time.

 

Thank you again and Happy New Year!







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