[An identification method of chromatin topological associated domains based on spatial density clustering].
Sheng Wu Yi Xue Gong Cheng Xue Za Zhi
; 41(3): 552-559, 2024 Jun 25.
Article
en Zh
| MEDLINE
| ID: mdl-38932542
ABSTRACT
The rapid development of high-throughput chromatin conformation capture (Hi-C) technology provides rich genomic interaction data between chromosomal loci for chromatin structure analysis. However, existing methods for identifying topologically associated domains (TADs) based on Hi-C data suffer from low accuracy and sensitivity to parameters. In this context, a TAD identification method based on spatial density clustering was designed and implemented in this paper. The method preprocessed the raw Hi-C data to obtain normalized Hi-C contact matrix data. Then, it computed the distance matrix between loci, generated a reachability graph based on the core distance and reachability distance of loci, and extracted clustering clusters. Finally, it extracted TAD boundaries based on clustering results. This method could identify TAD structures with higher coherence, and TAD boundaries were enriched with more ChIP-seq factors. Experimental results demonstrate that our method has advantages such as higher accuracy and practical significance in TAD identification.
Palabras clave
Texto completo:
1
Colección:
01-internacional
Banco de datos:
MEDLINE
Asunto principal:
Cromatina
Límite:
Humans
Idioma:
Zh
Revista:
Sheng Wu Yi Xue Gong Cheng Xue Za Zhi
/
Sheng wu yi xue gong cheng xue za zhi
Asunto de la revista:
ENGENHARIA BIOMEDICA
Año:
2024
Tipo del documento:
Article