{"updated":"2025-01-19T12:51:52.875849+00:00","metadata":{"_oai":{"id":"oai:ipsj.ixsq.nii.ac.jp:00225257","sets":["1164:5352:11207:11208"]},"path":["11208"],"owner":"44499","recid":"225257","title":["Multidimensional Scaling Methods Can Reconstruct Genomic DNA Loops Using Hi-C Data Properties"],"pubdate":{"attribute_name":"公開日","attribute_value":"2023-03-02"},"_buckets":{"deposit":"c39bd36b-da96-404b-9328-2d224ef53423"},"_deposit":{"id":"225257","pid":{"type":"depid","value":"225257","revision_id":0},"owners":[44499],"status":"published","created_by":44499},"item_title":"Multidimensional Scaling Methods Can Reconstruct Genomic DNA Loops Using Hi-C Data Properties","author_link":["595689","595690"],"item_titles":{"attribute_name":"タイトル","attribute_value_mlt":[{"subitem_title":"Multidimensional Scaling Methods Can Reconstruct Genomic DNA Loops Using Hi-C Data Properties"},{"subitem_title":"Multidimensional Scaling Methods Can Reconstruct Genomic DNA Loops Using Hi-C Data Properties","subitem_title_language":"en"}]},"item_type_id":"4","publish_date":"2023-03-02","item_4_text_3":{"attribute_name":"著者所属","attribute_value_mlt":[{"subitem_text_value":"Graduate School of Science and Engineering, Chuo University"}]},"item_4_text_4":{"attribute_name":"著者所属(英)","attribute_value_mlt":[{"subitem_text_value":"Graduate School of Science and Engineering, Chuo University","subitem_text_language":"en"}]},"item_language":{"attribute_name":"言語","attribute_value_mlt":[{"subitem_language":"eng"}]},"item_publisher":{"attribute_name":"出版者","attribute_value_mlt":[{"subitem_publisher":"情報処理学会","subitem_publisher_language":"ja"}]},"publish_status":"0","weko_shared_id":-1,"item_file_price":{"attribute_name":"Billing file","attribute_type":"file","attribute_value_mlt":[{"url":{"url":"https://ipsj.ixsq.nii.ac.jp/record/225257/files/IPSJ-BIO23073034.pdf","label":"IPSJ-BIO23073034.pdf"},"date":[{"dateType":"Available","dateValue":"2025-03-02"}],"format":"application/pdf","billing":["billing_file"],"filename":"IPSJ-BIO23073034.pdf","filesize":[{"value":"809.9 kB"}],"mimetype":"application/pdf","priceinfo":[{"tax":["include_tax"],"price":"660","billingrole":"5"},{"tax":["include_tax"],"price":"330","billingrole":"6"},{"tax":["include_tax"],"price":"0","billingrole":"41"},{"tax":["include_tax"],"price":"0","billingrole":"44"}],"accessrole":"open_date","version_id":"c25b776b-f28d-4177-88ba-b24751ea995a","displaytype":"detail","licensetype":"license_note","license_note":"Copyright (c) 2023 by the Information Processing Society of Japan"}]},"item_4_creator_5":{"attribute_name":"著者名","attribute_type":"creator","attribute_value_mlt":[{"creatorNames":[{"creatorName":"Ryo, Ishibashi"}],"nameIdentifiers":[{}]}]},"item_4_creator_6":{"attribute_name":"著者名(英)","attribute_type":"creator","attribute_value_mlt":[{"creatorNames":[{"creatorName":"Ryo, Ishibashi","creatorNameLang":"en"}],"nameIdentifiers":[{}]}]},"item_4_source_id_9":{"attribute_name":"書誌レコードID","attribute_value_mlt":[{"subitem_source_identifier":"AA12055912","subitem_source_identifier_type":"NCID"}]},"item_4_textarea_12":{"attribute_name":"Notice","attribute_value_mlt":[{"subitem_textarea_value":"SIG Technical Reports are nonrefereed and hence may later appear in any journals, conferences, symposia, etc."}]},"item_resource_type":{"attribute_name":"資源タイプ","attribute_value_mlt":[{"resourceuri":"http://purl.org/coar/resource_type/c_18gh","resourcetype":"technical report"}]},"item_4_source_id_11":{"attribute_name":"ISSN","attribute_value_mlt":[{"subitem_source_identifier":"2188-8590","subitem_source_identifier_type":"ISSN"}]},"item_4_description_7":{"attribute_name":"論文抄録","attribute_value_mlt":[{"subitem_description":"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.","subitem_description_type":"Other"}]},"item_4_description_8":{"attribute_name":"論文抄録(英)","attribute_value_mlt":[{"subitem_description":"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.","subitem_description_type":"Other"}]},"item_4_biblio_info_10":{"attribute_name":"書誌情報","attribute_value_mlt":[{"bibliographicPageEnd":"6","bibliographic_titles":[{"bibliographic_title":"研究報告バイオ情報学（BIO）"}],"bibliographicPageStart":"1","bibliographicIssueDates":{"bibliographicIssueDate":"2023-03-02","bibliographicIssueDateType":"Issued"},"bibliographicIssueNumber":"34","bibliographicVolumeNumber":"2023-BIO-73"}]},"relation_version_is_last":true,"weko_creator_id":"44499"},"created":"2025-01-19T01:24:46.155165+00:00","id":225257,"links":{}}