Question: Explanation of ENCODE SCREEN candidate cis-Regulatory elements classification
gravatar for yztxwd
14 months ago by
Southern Medical University
yztxwd380 wrote:

Hello everyone, I am confused with the explanation of ENCODE SCREEN candidate cis-regulatory elements (ccREs) classification. The description has been attached: SCREEN

According to the documents, they said for cell type-agnostic classification, ccREs will be divided into 3 groups, which are ccRE-PLS, ccRE-ELS and CTCF-only ccRE. Then for a specific individual cell type, all ccREs with low DNase Z-scores will be considered as "inactive" state, and the remaining "active" ccREs are divided into eight states according to their epigenetic signal Z-scores.

But the following words only mentioned 6 states: "inactive" state with low DNase Z-scores, ccRE-PLS, ccRE-ELS, CTCF-only ccRE, an "inactive" group (what's the difference with the "inactive" state?), a DNase-only group.

I have read the documents dozens of times but I am still not sure what exactly the 9 state is. Especially when I found the download page provides the "5 group" and "9 state XX" bed file, what does the "5 group" refer to? I appreciate any help to make this thing clear, thank you!

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