{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,7]],"date-time":"2025-11-07T13:35:37Z","timestamp":1762522537317,"version":"3.41.2"},"reference-count":43,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2021,4,14]],"date-time":"2021-04-14T00:00:00Z","timestamp":1618358400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/100010722","name":"Harbin Medical University","doi-asserted-by":"publisher","award":["YJSKYCX2019-30HYD"],"award-info":[{"award-number":["YJSKYCX2019-30HYD"]}],"id":[{"id":"10.13039\/100010722","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["81903186","32070673","61873075"],"award-info":[{"award-number":["81903186","32070673","61873075"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"National Key R&D Program of China","award":["2018YFC2000100"],"award-info":[{"award-number":["2018YFC2000100"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,9,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Consensus molecular subtypes (CMSs) are emerging as critical factor for prognosis and treatment of colorectal cancer. Gene regulators, including chromatin regulator, RNA-binding protein and transcriptional factor, are critical modulators of cancer hallmark, yet little is known regarding the underlying functional mechanism in CMSs. Herein, we identified a core set of 235 functional gene regulators (FGRs) by integrating genome, epigenome, transcriptome and interactome of CMSs. FGRs exhibited significant multi-omics alterations and impacts on cell lines growth, as well as significantly enriched cancer driver genes and pathways. Moreover, common FGRs played different roles in the context of CMSs. In accordance with the immune characteristics of CMSs, we found that the anti-tumor immune pathways were mainly activated by FGRs (e.g. STAT1 and CREBBP) in CMS1, while inhibited by FGRs in CMS2\u20134. FGRs mediated aberrant expression of ligands, which bind to receptor on immune cells, and modulated tumor immune microenvironment of subtypes. Intriguingly, systematic exploration of datasets using genomic and transcriptome co-similarity reveals the coordinated manner in FGRs act in CMSs to orchestrate their pathways and patients\u2019 prognosis. Expression signatures of the FGRs revealed an optimized CMS classifier, which demonstrated 88% concordance with the gold-standard classifier, but avoiding the influence of sample composition. Overall, our integrative analysis identified FGRs to regulate core tumorigenic processes\/pathways across CMSs.<\/jats:p>","DOI":"10.1093\/bib\/bbab077","type":"journal-article","created":{"date-parts":[[2021,2,19]],"date-time":"2021-02-19T12:25:44Z","timestamp":1613737544000},"source":"Crossref","is-referenced-by-count":7,"title":["Multilevel prioritization of gene regulators associated with consensus molecular subtypes of colorectal cancer"],"prefix":"10.1093","volume":"22","author":[{"given":"Kai","family":"Song","sequence":"first","affiliation":[{"name":"College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150086, China"}]},{"given":"Hao","family":"Cai","sequence":"additional","affiliation":[{"name":"Medical Big Data and Bioinformatics Research Center, First Affiliated Hospital of Gannan Medical University, Ganzhou, China"}]},{"given":"Hailong","family":"Zheng","sequence":"additional","affiliation":[{"name":"College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150086, China"}]},{"given":"Jing","family":"Yang","sequence":"additional","affiliation":[{"name":"College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150086, China"}]},{"given":"Liangliang","family":"Jin","sequence":"additional","affiliation":[{"name":"College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150086, China"}]},{"given":"Huiting","family":"Xiao","sequence":"additional","affiliation":[{"name":"College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150086, China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8953-8963","authenticated-orcid":false,"given":"Jiashuai","family":"Zhang","sequence":"additional","affiliation":[{"name":"College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150086, China"}]},{"given":"Zhangxiang","family":"Zhao","sequence":"additional","affiliation":[{"name":"College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150086, China"}]},{"given":"Xin","family":"Li","sequence":"additional","affiliation":[]},{"given":"Wenyuan","family":"Zhao","sequence":"additional","affiliation":[]},{"given":"Xia","family":"Li","sequence":"additional","affiliation":[{"name":"College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150086, China"}]}],"member":"286","published-online":{"date-parts":[[2021,4,14]]},"reference":[{"key":"2021090817334552900_ref1","doi-asserted-by":"crossref","first-page":"209","DOI":"10.1038\/ng.3214","article-title":"A big bang model of human colorectal tumor growth","volume":"47","author":"Sottoriva","year":"2015","journal-title":"Nat Genet"},{"key":"2021090817334552900_ref2","doi-asserted-by":"crossref","first-page":"1350","DOI":"10.1038\/nm.3967","article-title":"The consensus molecular subtypes of colorectal cancer","volume":"21","author":"Guinney","year":"2015","journal-title":"Nat 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