are there any downloadable database for tissue specific DMRs?

Question

[pt.taklifi]

Hello everyone , I am trying to find DMRs between some somatic tissues ( for example breast , liver, lung ,etc) and normal blood ( i.e. breast vs blood, liver vs blood ,..) . Although I have seen a lot of studies such as this one , I have trouble finding a downloadable dataset that provides locations of t-DMRs. I was wondering if anyone knows of such a database ?

Answer 1

[abcoxyzide]

Not exactly what you're looking for, but I recently came across this paper that does deconvolution based on methylation signatures. They identified a set of CpGs which they called tissue informative markers (TIMs) using public data, and used that for cell type deconvolution.

You may wanna have a look at their github repo and see if that suits your need. Good luck!

Answer 2

[yupeng he]

You may this dataset useful. https://www.nature.com/articles/nature14465

The processed data and code are downloadable under this website. http://neomorph.salk.edu/human_tissue_methylomes.html

Specifically, it is the "code and processed data" link under this page: http://neomorph.salk.edu/SDEC_tissue_methylomes/processed_data/index.html

After unzipping, DMR_by_methylpy/DMR_methylpy_matrix.tsv and the files under DMR_hypo_hyper are the DMRs identified across all tissues in the dataset.