Multidimensional Scaling Methods Can Reconstruct Genomic DNA Loops Using Hi-C Data Properties

• Item type: SIG Technical Reports(1)
• 公開日: 2023-03-02
• タイトル: Multidimensional Scaling Methods Can Reconstruct Genomic DNA Loops Using Hi-C Data Properties
• タイトル / 言語: en
• タイトル: Multidimensional Scaling Methods Can Reconstruct Genomic DNA Loops Using Hi-C Data Properties
• 言語: eng
• 資源タイプ / 資源タイプ識別子: http://purl.org/coar/resource_type/c_18gh
• 資源タイプ: technical report
• 著者所属: Graduate School of Science and Engineering, Chuo University
• 著者所属(英): en
• 著者所属(英): Graduate School of Science and Engineering, Chuo University
• 著者名: Ryo, Ishibashi
• 著者名(英): Ryo, Ishibashi
• 論文抄録 / 内容記述タイプ: Other
• 論文抄録 / 内容記述: This paper proposes the application of multidimensional scaling (MDS) to Hi-C data on genomic interactions as a method of visualizing DNA loops. Currently, the mechanisms underlying the regulation of gene expression are poorly understood. Previous studies have focused on reproducing the entire three-dimensional structure of chromatin; however, identifying DNA loops using such data is time-consuming and difficult. Hi-C data were converted to distances by taking the inverse to reproduce loops via MDS, and missing values were set to zero. MDS was applied to the log-transformed genomic coordinate distances using the converted data, and this process successfully reproduced the DNA loops in the given structure. Consequently, the reconstructed DNA loops contained significantly more DNA bound by transcription factors involved in DNA loop formation than that obtained using previously applied methods. In conclusion, the proposed method represents an improvement over previous methods.
• 論文抄録(英) / 内容記述タイプ: Other
• 論文抄録(英) / 内容記述: This paper proposes the application of multidimensional scaling (MDS) to Hi-C data on genomic interactions as a method of visualizing DNA loops. Currently, the mechanisms underlying the regulation of gene expression are poorly understood. Previous studies have focused on reproducing the entire three-dimensional structure of chromatin; however, identifying DNA loops using such data is time-consuming and difficult. Hi-C data were converted to distances by taking the inverse to reproduce loops via MDS, and missing values were set to zero. MDS was applied to the log-transformed genomic coordinate distances using the converted data, and this process successfully reproduced the DNA loops in the given structure. Consequently, the reconstructed DNA loops contained significantly more DNA bound by transcription factors involved in DNA loop formation than that obtained using previously applied methods. In conclusion, the proposed method represents an improvement over previous methods.
• 書誌レコードID / 収録物識別子タイプ: NCID
• 書誌レコードID / 収録物識別子: AA12055912
• 書誌情報: 研究報告バイオ情報学（BIO）; 巻 2023-BIO-73, 号 34, p. 1-6, 発行日 2023-03-02
• ISSN / 収録物識別子タイプ: ISSN
• ISSN / 収録物識別子: 2188-8590
• Notice: SIG Technical Reports are nonrefereed and hence may later appear in any journals, conferences, symposia, etc.
• 出版者 / 言語: ja
• 出版者: 情報処理学会