Interpretable online network dictionary learning for inferring long-range chromatin interactions
Fig 5
Dictionary elements for Drosophila chromosomes 2L, 2R, 3L and 3R obtained using online cvxNDL.
Each subplot contains 25 dictionary elements for the corresponding chromosome and each block in the subplots corresponds to one dictionary element. The elements are ordered by their importance score. Note that the “diagonals” in the dictionary elements do not exclusively represent localized topologically associated domains (TADs) as in standard chromatin contact maps; instead, they can also capture long-range interactions. This is due to the fact that the indices of the dictionary element matrices represent genomic regions that may be far apart in the genome. In contrast, standard contact maps have indices that correspond to continuously ordered genomic regions, so that the diagonals truly represent TADs (see Fig 4). The color-code captures the actual locations of the genomic regions involved in the representatives and their dictionary elements. The most interesting dictionary elements are those that contain both dark blue, light blue/green, and red colors (since they involve long-range interactions). This is especially the case for chr3L and chr3R.