The candidate cis-regulatory regions (cCREs) called using IDEAS in IS mode. 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 is a union and merge of the cCREs called in all the cell types used in the joint human-mouse IDEAS segmentation. The cCRE is colored by the evolutionary categories, with sequence and function conserved (SF) being red, sequence conserved (S) green, and not sequence conserved (N) being blue. The label is the evolutionary category and the joint metacluster (JmC). The JmC groups cCREs with similar activity profiles across blood cell types in both human and mouse.
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
Last updated Sept 2021