This track shows topologically associating domains (TADs), the original "topological domains" defined by Dixon et al. 2012, in two human cell types: H1 human embryonic stem cells (hESC) and IMR90 fetal lung fibroblasts. A domain is a contiguous region that preferentially interacts with itself in Hi-C data.
Domains were called from Hi-C data analyzed in fixed-size 40 kb bins, so domain edges are uncertain to roughly ±20 kb. Domains cover roughly 86–91% of the genome, and the gaps between domains are what Dixon et al. call "topological boundaries" (under 400 kb) or "unorganized chromatin" (over 400 kb). No per-domain confidence score is published by the authors, so none is shown. These coordinates are not directly comparable to the other TAD tracks.
Domains were identified with a directionality-index hidden Markov model on 40 kb Hi-C contact matrices (Dixon et al., 2012). The published combined-replicate domain calls (Supplementary Table S3) were obtained for hESC and IMR90, originally on assembly hg18/NCBI36, and lifted to this assembly with the UCSC liftOver tool; a small fraction of domains that did not map cleanly were dropped. Lifted domains that came out more than twice their original size were also removed, because this happens when a domain spans a gap or a rearranged region between the two assemblies.
The raw data can be explored interactively with the Table Browser or the Data Integrator. For programmatic access, the track can be accessed using the Genome Browser's REST API. The underlying bigBed files can be downloaded from our download server.
Dixon JR, Selvaraj S, Yue F, Kim A, Li Y, Shen Y, Hu M, Liu JS, Ren B. Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature. 2012 Apr 11;485(7398):376-80. DOI: 10.1038/nature11082; PMID: 22495300; PMC: PMC3356448