Department of Biosciences, University of Oslo, 0316 Oslo, Norway.
Centre for Bioinformatics, Department of Informatics, University of Oslo, 0316 Oslo, Norway.
Brief Bioinform. 2023 Sep 20;24(5). doi: 10.1093/bib/bbad302.
The three-dimensional organization of chromatin plays a crucial role in gene regulation and cellular processes like deoxyribonucleic acid (DNA) transcription, replication and repair. Hi-C and related techniques provide detailed views of spatial proximities within the nucleus. However, data analysis is challenging partially due to a lack of well-defined, underpinning mathematical frameworks. Recently, recognizing and analyzing geometric patterns in Hi-C data has emerged as a powerful approach. This review provides a summary of algorithms for automatic recognition and analysis of geometric patterns in Hi-C data and their correspondence with chromatin structure. We classify existing algorithms on the basis of the data representation and pattern recognition paradigm they make use of. Finally, we outline some of the challenges ahead and promising future directions.
染色质的三维组织在基因调控和细胞过程中起着至关重要的作用，如脱氧核糖核酸（DNA）转录、复制和修复。Hi-C 和相关技术提供了细胞核内空间接近度的详细视图。然而，由于缺乏明确的、基础的数学框架，数据分析具有一定的挑战性。最近，在 Hi-C 数据中识别和分析几何模式已成为一种强大的方法。本文综述了用于自动识别和分析 Hi-C 数据中的几何模式及其与染色质结构对应关系的算法。我们根据它们所利用的数据表示和模式识别范例对现有算法进行分类。最后，我们概述了未来的一些挑战和有前途的方向。
