{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,25]],"date-time":"2026-02-25T22:19:13Z","timestamp":1772057953272,"version":"3.50.1"},"reference-count":39,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2025,2,5]],"date-time":"2025-02-05T00:00:00Z","timestamp":1738713600000},"content-version":"vor","delay-in-days":75,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100012166","name":"National Key Research and Development Program of China","doi-asserted-by":"publisher","award":["2020YFA0712400"],"award-info":[{"award-number":["2020YFA0712400"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Science Foundation of China","doi-asserted-by":"publisher","award":["11931008"],"award-info":[{"award-number":["11931008"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,11,22]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Biclustering has emerged as a promising approach for analyzing high-dimensional expression data, offering unique advantages in uncovering localized co-expression patterns that traditional clustering methods often miss and thus facilitating advancements in complex disease research and other biomedical applications. However, state-of-the-art methods identify distinct patterns at the expense of losing information about specific patterns, some of which have been used to define cancer subtypes or reflect the progression of a disease or cellular processes. Additionally, these methods exhibit poor effectiveness in noisy environments. To address these limitations, we propose the bucket trend-preserving (BTP) pattern, a novel generalization of existing patterns. And we have developed an algorithm, TransBic, to extract significant biclusters of BTP-patterns. Specifically, TransBic transforms the problem into identifying common multipartite acyclic tournament subdigraphs shared by distinct subsets of acyclic tournament digraphs derived from a given expression matrix. Compared with prominent tools, TransBic demonstrates superior performance in identifying biclusters of all non-row-constant patterns, especially under noise and data fluctuations. Furthermore, TransBic successfully identifies the most disease-related pathways for type 2 diabetes (T2D), colorectal cancer, hepatocellular carcinoma, and breast cancer, outperforming other tools in this regard. Different from previous generalizations, BTP-patterns capture specific up-regulation and down-regulation dynamics. Through targeted analysis of BTP-patterns in T2D expression data, TransBic uncovers biological processes affected by disease risk factors, extending the application of trend-preserving biclustering in expression data analysis.<\/jats:p>","DOI":"10.1093\/bib\/bbaf050","type":"journal-article","created":{"date-parts":[[2025,2,5]],"date-time":"2025-02-05T06:34:11Z","timestamp":1738737251000},"source":"Crossref","is-referenced-by-count":1,"title":["TransBic: bucket trend-preserving biclustering for finding local and interpretable expression patterns"],"prefix":"10.1093","volume":"26","author":[{"given":"Jing","family":"Li","sequence":"first","affiliation":[{"name":"Research Center for Mathematics and Interdisciplinary Sciences , Shandong University, No. 72 Binhai Road, Jimo Distinct, Qingdao 266237, Shandong,","place":["China"]},{"name":"Institute of Systems Engineering , PLA Academy of Military Sciences, No. 28 Xizhimen North Street, Haidian Distinct, Beijing 100082,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Qinglin","family":"Mei","sequence":"additional","affiliation":[{"name":"MOE key Laboratory of Bioinformatics , BNRIST Bioinformatics Division, Department of Automation, Tsinghua University, No. 30 Shuangqing Road, Beijing 100084,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chaoxia","family":"Yang","sequence":"additional","affiliation":[{"name":"College of Science , Nanjing University of Posts and Telecommunications, No. 9 Wenyuan Road, Yadong New City District, Nanjing 210023, Jiangsu,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Naibo","family":"Zhu","sequence":"additional","affiliation":[{"name":"Institute of Systems Engineering , PLA Academy of Military Sciences, No. 28 Xizhimen North Street, Haidian Distinct, Beijing 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