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Literature DB >> 29334377

Detecting hierarchical genome folding with network modularity.

Heidi K Norton¹, Daniel J Emerson¹, Harvey Huang¹, Jesi Kim¹, Katelyn R Titus¹, Shi Gu^1,2, Danielle S Bassett^1,3, Jennifer E Phillips-Cremins^1,4,5.

Abstract

Mammalian genomes are folded in a hierarchy of compartments, topologically associating domains (TADs), subTADs and looping interactions. Here, we describe 3DNetMod, a graph theory-based method for sensitive and accurate detection of chromatin domains across length scales in Hi-C data. We identify nested, partially overlapping TADs and subTADs genome wide by optimizing network modularity and varying a single resolution parameter. 3DNetMod can be applied broadly to understand genome reconfiguration in development and disease.

Entities: Chemical Disease Gene Species

Mesh：

Substances：
Chromatin

Year: 2018 PMID： 29334377 PMCID： PMC6029251 DOI： 10.1038/nmeth.4560

Source DB: PubMed Journal: Nat Methods ISSN： 1548-7091 Impact factor: 28.547

24 in total

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10. The methyltransferase SETDB1 regulates a large neuron-specific topological chromatin domain.

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3. MSTD: an efficient method for detecting multi-scale topological domains from symmetric and asymmetric 3D genomic maps.

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4. BHi-Cect: a top-down algorithm for identifying the multi-scale hierarchical structure of chromosomes.

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Review 5. Chromosome Conformation Capture and Beyond: Toward an Integrative View of Chromosome Structure and Function.

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