We define a candidate cis-regulatory element, or cCRE, as a DNA interval with a high signal for chromatin accessibility in any cell type (Xiang et al. 2020). We utilized a version of the IDEAS methodology to combine peaks of accessibility across different cell types, running it in the signal intensity state (IS) mode only on chromatin accessibility signals (Xiang et al. 2021), which helps counteract excessive expansion of peak calls when combining them.
This track shows the intensity states (IS).
An integrative view of the regulatory and transcriptional landscapes in mouse hematopoiesis. Guanjue Xiang, et al. 2020. PMID: 32132109
S3V2-IDEAS: a package for normalizing, denoising and integrating epigenomic datasets across different cell types. Guanjue Xiang, et al. 2021, PMID: 33681991
Interspecies regulatory landscapes and elements revealed by novel joint systematic integration of human and mouse blood cell epigenomes. Guanjue Xiang, et al. biorxiv