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These technologies not only offer new insight into high-dimensional chromatin organization and gene regulation, but also introduce new challenges in data visualization and analysis. To overcome these challenges, we developed MCIBox, a toolkit for multi-way chromatin interaction (MCI) analysis, including a visualization tool and a platform for identifying micro-domains with clustered single-molecule chromatin complexes. MCIBox is based on various clustering algorithms integrated with dimensionality reduction methods that can display multiplex chromatin interactions at single-molecule level, allowing users to explore chromatin extrusion patterns and super-enhancers regulation modes in transcription, and to identify single-molecule chromatin complexes that are clustered into micro-domains. Furthermore, MCIBox incorporates a two-dimensional kernel density estimation algorithm to identify micro-domains boundaries automatically. These micro-domains were stratified with distinctive signatures of transcription activity and contained different cell-cycle-associated genes. Taken together, MCIBox represents an invaluable tool for the study of multiple chromatin interactions and inaugurates a previously unappreciated view of 3D genome structure.<\/jats:p>","DOI":"10.1093\/bib\/bbac380","type":"journal-article","created":{"date-parts":[[2022,8,24]],"date-time":"2022-08-24T13:32:42Z","timestamp":1661347962000},"source":"Crossref","is-referenced-by-count":7,"title":["MCIBox: a toolkit for single-molecule multi-way chromatin interaction visualization and micro-domains identification"],"prefix":"10.1093","volume":"23","author":[{"given":"Simon Zhongyuan","family":"Tian","sequence":"first","affiliation":[{"name":"Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Department of Biology, School of Life Sciences, Southern University of Science and Technology , 1088 Xueyuan Rd, Nanshan District, Shenzhen, 518055, Guangdong, China"}]},{"given":"Guoliang","family":"Li","sequence":"additional","affiliation":[{"name":"National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University , No.1 Shizishan Street, Hongshan District, Wuhan, 430070, Hubei, China"},{"name":"Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, 3D Genomics Research Center, College of Informatics, Huazhong Agricultural University , No.1, Shizishan Street, Hongshan District, Wuhan, 430070, Hubei, China"}]},{"given":"Duo","family":"Ning","sequence":"additional","affiliation":[{"name":"Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Department of Biology, School of Life Sciences, Southern University of Science and Technology , 1088 Xueyuan Rd, Nanshan District, Shenzhen, 518055, Guangdong, China"}]},{"given":"Kai","family":"Jing","sequence":"additional","affiliation":[{"name":"Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Department of Biology, School of Life Sciences, Southern University of Science and Technology , 1088 Xueyuan Rd, Nanshan District, Shenzhen, 518055, Guangdong, China"}]},{"given":"Yewen","family":"Xu","sequence":"additional","affiliation":[{"name":"Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Department of Biology, School of Life Sciences, Southern University of Science and Technology , 1088 Xueyuan Rd, Nanshan District, Shenzhen, 518055, Guangdong, China"}]},{"given":"Yang","family":"Yang","sequence":"additional","affiliation":[{"name":"Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Department of Biology, School of Life Sciences, Southern University of Science and Technology , 1088 Xueyuan Rd, Nanshan District, Shenzhen, 518055, Guangdong, China"}]},{"given":"Melissa J","family":"Fullwood","sequence":"additional","affiliation":[{"name":"School of Biological Sciences, Nanyang Technological University , 60 Nanyang Dr, 637551, Singapore"},{"name":"Cancer Science Institute of Singapore, National University of Singapore , 14 Medical Dr, 117599, Singapore"},{"name":"Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR) , 61 Biopolis Dr, 138673, Singapore"}]},{"given":"Pengfei","family":"Yin","sequence":"additional","affiliation":[{"name":"Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Department of Biology, School of Life Sciences, Southern University of Science and Technology , 1088 Xueyuan Rd, Nanshan District, Shenzhen, 518055, Guangdong, China"}]},{"given":"Guangyu","family":"Huang","sequence":"additional","affiliation":[{"name":"Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Department of Biology, School of Life Sciences, Southern University of Science and Technology , 1088 Xueyuan Rd, Nanshan District, Shenzhen, 518055, Guangdong, China"}]},{"given":"Dariusz","family":"Plewczynski","sequence":"additional","affiliation":[{"name":"Laboratory of Bioinformatics and Computational Genomics, Faculty of Mathematics and Information Science, Warsaw University of Technology , Pl. 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