Question: Encode Genome Browser: How To Correlate Dnasei Hypersensitivity With Rna-Seq?
gravatar for khandarius
7.2 years ago by
khandarius0 wrote:

Hi! I'm interested in exploring the relationship of certain genes' expression and DNaseI hypersensitivity of their promoter regions. I would like to correlate hypersensitivity data with measures of gene activity such as RNA-seq data. I'm using the UCSC genome browser with ENCODE data but I have some problems. I can't seem to find data with comparable signal values in the Table Browser - the formats are such that the correlate -function can't be used. I can get signal peak values for DNaseI hypersensitivity but the RNA-seq tables just describe sequence reads. I'd be grateful for any advice on how to proceed.


data encode • 2.3k views
ADD COMMENTlink modified 7.2 years ago by Alex Reynolds30k • written 7.2 years ago by khandarius0

ENCODE and correlation are antonyms. I've heard from several people that the ENCODE data cannot be compared between different experiments.

ADD REPLYlink written 7.2 years ago by Asaf8.3k
gravatar for Alex Reynolds
7.2 years ago by
Alex Reynolds30k
Seattle, WA USA
Alex Reynolds30k wrote:

Perhaps you could bin your RNAseq reads, creating windowed signal that you can correlate with the DNaseI data. You probably want to match the DNaseI window step and width parameters, so that you are correlating apples with apples.

ADD COMMENTlink written 7.2 years ago by Alex Reynolds30k

Thanks for the tip - especially pointing me to bedops, the suite is very useful. I need peak signal values for transcript abundance, though. I think I'll try to extract the FPKM values of a transcript for different cell lines and correlate those with the hypersensitivity peaks of corresponding transcript TSS.

ADD REPLYlink written 7.2 years ago by khandarius0
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