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SuperTAD: robust detection of hierarchical topologically associated domains with optimized structural information.


ABSTRACT: Topologically associating domains (TADs) are the organizational units of chromosome structures. TADs can contain TADs, thus forming a hierarchy. TAD hierarchies can be inferred from Hi-C data through coding trees. However, the current method for computing coding trees is not optimal. In this paper, we propose optimal algorithms for this computation. In comparison with seven state-of-art methods using two public datasets, from GM12878 and IMR90 cells, SuperTAD shows a significant enrichment of structural proteins around detected boundaries and histone modifications within TADs and displays a high consistency between various resolutions of identical Hi-C matrices.

SUBMITTER: Zhang YW 

PROVIDER: S-EPMC7831269 | biostudies-literature | 2021 Jan

REPOSITORIES: biostudies-literature

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SuperTAD: robust detection of hierarchical topologically associated domains with optimized structural information.

Zhang Yu Wei YW   Wang Meng Bo MB   Li Shuai Cheng SC  

Genome biology 20210125 1


Topologically associating domains (TADs) are the organizational units of chromosome structures. TADs can contain TADs, thus forming a hierarchy. TAD hierarchies can be inferred from Hi-C data through coding trees. However, the current method for computing coding trees is not optimal. In this paper, we propose optimal algorithms for this computation. In comparison with seven state-of-art methods using two public datasets, from GM12878 and IMR90 cells, SuperTAD shows a significant enrichment of st  ...[more]

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