-This track holds the DANIO-CODE annotation of candidate regulatory elements, at five +This track is part of the DANIO-CODE track collection. +It holds the consortium's annotation of candidate regulatory elements, at five developmental stages: Dome, 75% epiboly, 5-9 somites, Prim-5 and Long-pec. Four related annotations are shown for each stage.
ChromHMM is a segmentation of the whole genome into ten chromatin states. The segmentation is learned from the combination of histone modifications present at each position, and each state was then given a name by hand, using the Roadmap Epigenomics annotation as a reference: active transcription start sites, their flanking regions, active and primed enhancers, poised elements, Polycomb-repressed regions and a quiescent state with no detectable mark.
PADREs are predicted ATAC-supported developmental regulatory elements: the subset of the segmentation that also lies in a region of open chromatin, which is the consortium's set of candidate regulatory elements. Across all stages there are more than 140,000 of them. cPADREs are the consensus set of 83,553 elements that are called at every stage, so they can be compared position by position across development. DOPEs are dynamic orphan predicted elements: regions that are open at a given stage but carry no histone mark at all.
--This track is part of the DANIO-CODE collection. -
-Each combination of annotation type and developmental stage is a separate track. On the configuration page they are laid out as a grid, with the annotation type across and the stage down. Only the ChromHMM tracks are checked when the grid is first opened.
The ChromHMM and PADRE tracks are colored by chromatin state:
| 1_TssA1 — active transcription start site |