+This track is part of the DANIO-CODE track collection. A chromosome is not a straight line in the nucleus. It is folded so that some parts touch each other far more often than others, and the regions of preferential contact are called topologically associating domains. Domain boundaries matter for gene regulation, because an enhancer usually acts on genes inside its own domain and rarely across a boundary. Hi-C measures which parts of the genome are in contact by crosslinking, cutting and religating chromatin, then sequencing the resulting pairs.
This track does not show the contact matrix itself but two summary scores computed from it along the genome. The insulation index is low where few contacts cross a position, so its local minima mark domain boundaries. The directionality index measures whether the contacts at a position point mostly upstream or mostly downstream, and it flips sign at a boundary. Both are shown for 4 samples at 4 developmental stages (256-cell, Dome, 75% epiboly and Prim-5) and at three window sizes, 50 kb, 500 kb and 1 Mb.
--This track is part of the DANIO-CODE collection. -
-Each combination of sample, index type and window size is a separate auto-scaled graph. Positive values are drawn in red and negative values in blue. The window size sets the scale at which the index is computed, so the 50 kb tracks respond to local boundaries and the 1 Mb tracks to large-scale compartments.
Nothing is displayed until tracks are selected on the configuration page, where they can be filtered by developmental stage, window size, index type and sample.