{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,28]],"date-time":"2026-07-28T00:33:37Z","timestamp":1785198817170,"version":"3.55.0"},"reference-count":53,"publisher":"Oxford University Press (OUP)","issue":"23","license":[{"start":{"date-parts":[[2021,7,10]],"date-time":"2021-07-10T00:00:00Z","timestamp":1625875200000},"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\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["11871026"],"award-info":[{"award-number":["11871026"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["11871237"],"award-info":[{"award-number":["11871237"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["61602309"],"award-info":[{"award-number":["61602309"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Hubei Provincial Science and Technology Innovation Base (Platform) Special Project","award":["2020DFH002"],"award-info":[{"award-number":["2020DFH002"]}]},{"DOI":"10.13039\/501100017607","name":"Shenzhen Fundamental Research Program","doi-asserted-by":"publisher","award":["JCYJ20170817095210760"],"award-info":[{"award-number":["JCYJ20170817095210760"]}],"id":[{"id":"10.13039\/501100017607","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100021171","name":"Guangdong Basic and Applied Basic Research Foundation","doi-asserted-by":"publisher","award":["2019A1515011384"],"award-info":[{"award-number":["2019A1515011384"]}],"id":[{"id":"10.13039\/501100021171","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Hong Kong Research Grants Council","award":["11200818"],"award-info":[{"award-number":["11200818"]}]},{"name":"Hong Kong Innovation and Technology Commission"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,12,7]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Differential network analysis is an important tool to investigate the rewiring of gene interactions under different conditions. Several computational methods have been developed to estimate differential networks from gene expression data, but most of them do not consider that gene network rewiring may be driven by the differential expression of individual genes. New differential network analysis methods that simultaneously take account of the changes in gene interactions and changes in expression levels are needed.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>: In this article, we propose a differential network analysis method that considers the differential expression of individual genes when identifying differential edges. First, two hypothesis test statistics are used to quantify changes in partial correlations between gene pairs and changes in expression levels for individual genes. Then, an optimization framework is proposed to combine the two test statistics so that the resulting differential network has a hierarchical property, where a differential edge can be considered only if at least one of the two involved genes is differentially expressed. Simulation results indicate that our method outperforms current state-of-the-art methods. We apply our method to identify the differential networks between the luminal A and basal-like subtypes of breast cancer and those between acute myeloid leukemia and normal samples. Hub nodes in the differential networks estimated by our method, including both differentially and nondifferentially expressed genes, have important biological functions.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>All the datasets underlying this article are publicly available. Processed data and source code can be accessed through the Github repository at https:\/\/github.com\/Zhangxf-ccnu\/chNet.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btab502","type":"journal-article","created":{"date-parts":[[2021,7,5]],"date-time":"2021-07-05T11:33:24Z","timestamp":1625484804000},"page":"4414-4423","source":"Crossref","is-referenced-by-count":27,"title":["Differential network analysis by simultaneously considering changes in gene interactions and gene expression"],"prefix":"10.1093","volume":"37","author":[{"given":"Jia-Juan","family":"Tu","sequence":"first","affiliation":[{"name":"School of Mathematics and Statistics and Hubei Key Laboratory of Mathematical Sciences, Central China Normal University , Wuhan 430079, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Le","family":"Ou-Yang","sequence":"additional","affiliation":[{"name":"College of Electronics and Information Engineering, Shenzhen University , Shenzhen 518060, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1372-9135","authenticated-orcid":false,"given":"Yuan","family":"Zhu","sequence":"additional","affiliation":[{"name":"School of Automation, China University of Geosciences , Wuhan 430074, China"},{"name":"Hubei Key Laboratory of Advanced Control and Intelligent Automation for Complex Systems, China University of Geosciences , Wuhan 430074, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hong","family":"Yan","sequence":"additional","affiliation":[{"name":"Department of Electrical Engineering, City University of Hong Kong , Hong Kong, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hong","family":"Qin","sequence":"additional","affiliation":[{"name":"Department of Statistics, Zhongnan University of Economics and Law , Wuhan 430073, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5052-9725","authenticated-orcid":false,"given":"Xiao-Fei","family":"Zhang","sequence":"additional","affiliation":[{"name":"School of Mathematics and Statistics and Hubei Key Laboratory of Mathematical Sciences, Central China Normal University , Wuhan 430079, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2021,7,10]]},"reference":[{"key":"2023061310492493400_btab502-B1","doi-asserted-by":"crossref","first-page":"56","DOI":"10.1038\/nrg2918","article-title":"Network medicine: a network-based approach to human disease","volume":"12","author":"Barab\u00e1si","year":"2011","journal-title":"Nat. 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