{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,26]],"date-time":"2025-10-26T15:04:14Z","timestamp":1761491054102,"version":"3.37.3"},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2020,7,27]],"date-time":"2020-07-27T00:00:00Z","timestamp":1595808000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100012166","name":"National Key R&D Program of China","doi-asserted-by":"crossref","award":["2018YFC0910500"],"award-info":[{"award-number":["2018YFC0910500"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["81672736"],"award-info":[{"award-number":["81672736"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Shanghai Municipal Science and Technology","award":["2017SHZDZX01","18DZ2294200"],"award-info":[{"award-number":["2017SHZDZX01","18DZ2294200"]}]},{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,4,20]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Dysfunctional regulations of gene expression programs relevant to fundamental cell processes can drive carcinogenesis. Therefore, systematically identifying dysregulation events is an effective path for understanding carcinogenesis and provides insightful clues to build predictive signatures with mechanistic interpretability for cancer precision medicine. Here, we implemented a machine learning-based gene dysregulation analysis framework in an R package, DysRegSig, which is capable of exploring gene dysregulations from high-dimensional data and building mechanistic signature based on gene dysregulations. DysRegSig can serve as an easy-to-use tool to facilitate gene dysregulation analysis and follow-up analysis.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The source code and user\u2019s guide of DysRegSig are freely available at Github: https:\/\/github.com\/SCBIT-YYLab\/DysRegSig.<\/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\/btaa688","type":"journal-article","created":{"date-parts":[[2020,7,23]],"date-time":"2020-07-23T11:30:05Z","timestamp":1595503805000},"page":"429-430","source":"Crossref","is-referenced-by-count":2,"title":["DysRegSig: an R package for identifying gene dysregulations and building mechanistic signatures in cancer"],"prefix":"10.1093","volume":"37","author":[{"given":"Quanxue","family":"Li","sequence":"first","affiliation":[{"name":"School of Biotechnology, East China University of Science and Technology , Shanghai 200237, China"},{"name":"Shanghai Center for Bioinformation Technology , Shanghai 201203, China"}]},{"given":"Wentao","family":"Dai","sequence":"additional","affiliation":[{"name":"Shanghai Center for Bioinformation Technology , Shanghai 201203, China"},{"name":"Department of Surgery, Shanghai Key Laboratory of Gastric Neoplasms, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine , Shanghai 200020, China"},{"name":"Shanghai Engineering Research Center of Pharmaceutical Translation, Shanghai Industrial Technology Institute , Shanghai 201203, China"}]},{"given":"Jixiang","family":"Liu","sequence":"additional","affiliation":[{"name":"Shanghai Center for Bioinformation Technology , Shanghai 201203, China"},{"name":"Shanghai Engineering Research Center of Pharmaceutical Translation, Shanghai Industrial Technology Institute , Shanghai 201203, China"}]},{"given":"Qingqing","family":"Sang","sequence":"additional","affiliation":[{"name":"Department of Surgery, Shanghai Key Laboratory of Gastric Neoplasms, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine , Shanghai 200020, China"}]},{"given":"Yi-Xue","family":"Li","sequence":"additional","affiliation":[{"name":"School of Biotechnology, East China University of Science and Technology , Shanghai 200237, China"},{"name":"Shanghai Center for Bioinformation Technology , Shanghai 201203, China"},{"name":"Shanghai Engineering Research Center of Pharmaceutical Translation, Shanghai Industrial Technology Institute , Shanghai 201203, China"},{"name":"CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences , Shanghai 200031, China"}]},{"given":"Yuan-Yuan","family":"Li","sequence":"additional","affiliation":[{"name":"Shanghai Center for Bioinformation Technology , Shanghai 201203, China"},{"name":"Shanghai Engineering Research Center of Pharmaceutical Translation, Shanghai Industrial Technology Institute , Shanghai 201203, China"}]}],"member":"286","published-online":{"date-parts":[[2020,7,27]]},"reference":[{"key":"2023051603583105100_btaa688-B1","doi-asserted-by":"crossref","first-page":"629","DOI":"10.1016\/j.cell.2016.12.013","article-title":"Transcriptional addiction in cancer","volume":"168","author":"Bradner","year":"2017","journal-title":"Cell"},{"key":"2023051603583105100_btaa688-B2","doi-asserted-by":"crossref","first-page":"326","DOI":"10.1016\/j.tig.2010.05.001","article-title":"From \u2018differential expression\u2019 to \u2018differential networking\u2019 \u2013 identification of dysfunctional regulatory networks in diseases","volume":"26","author":"de la Fuente","year":"2010","journal-title":"Trends Genet. TIG"},{"key":"2023051603583105100_btaa688-B3","doi-asserted-by":"crossref","first-page":"646","DOI":"10.1016\/j.cell.2011.02.013","article-title":"Hallmarks of cancer: the next generation","volume":"144","author":"Hanahan","year":"2011","journal-title":"Cell"},{"key":"2023051603583105100_btaa688-B4","first-page":"2869","article-title":"Confidence intervals and hypothesis testing for high-dimensional regression","volume":"15","author":"Javanmard","year":"2014","journal-title":"J. Mach. Learn. Res"},{"key":"2023051603583105100_btaa688-B5","doi-asserted-by":"crossref","first-page":"13","DOI":"10.18637\/jss.v036.i11","article-title":"Feature selection with the Boruta package","volume":"36","author":"Kursa","year":"2010","journal-title":"J. Stat. Softw"},{"key":"2023051603583105100_btaa688-B6","doi-asserted-by":"crossref","first-page":"1237","DOI":"10.1016\/j.cell.2013.02.014","article-title":"Transcriptional regulation and its misregulation in disease","volume":"152","author":"Lee","year":"2013","journal-title":"Cell"},{"key":"2023051603583105100_btaa688-B7","doi-asserted-by":"crossref","first-page":"12","DOI":"10.1016\/j.artmed.2017.02.006","article-title":"Differential regulation analysis reveals dysfunctional regulatory mechanism involving transcription factors and microRNAs in gastric carcinogenesis","volume":"77","author":"Li","year":"2017","journal-title":"Artif. Intell. Med"},{"key":"2023051603583105100_btaa688-B8","doi-asserted-by":"crossref","first-page":"544","DOI":"10.1038\/nature25501","article-title":"TGFbeta attenuates tumour response to PD-L1 blockade by contributing to exclusion of T cells","volume":"554","author":"Mariathasan","year":"2018","journal-title":"Nature"},{"key":"2023051603583105100_btaa688-B9","doi-asserted-by":"crossref","first-page":"267","DOI":"10.1038\/nrrheum.2013.14","article-title":"Mechanistic biomarkers for clinical decision making in rheumatic diseases","volume":"9","author":"Robinson","year":"2013","journal-title":"Nat. Rev. Rheumatol"},{"key":"2023051603583105100_btaa688-B10","doi-asserted-by":"crossref","first-page":"1013","DOI":"10.1007\/s00018-017-2679-6","article-title":"Differential gene regulatory networks in development and disease","volume":"75","author":"Singh","year":"2018","journal-title":"Cell Mol. Life Sci"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btaa688\/33750817\/btaa688.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/37\/3\/429\/50326125\/btaa688.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/37\/3\/429\/50326125\/btaa688.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,5,16]],"date-time":"2023-05-16T03:59:25Z","timestamp":1684209565000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/37\/3\/429\/5876822"}},"subtitle":[],"editor":[{"given":"Pier","family":"Luigi Martelli","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2020,7,27]]},"references-count":10,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2021,4,20]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btaa688","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"type":"print","value":"1367-4803"},{"type":"electronic","value":"1367-4811"}],"subject":[],"published-other":{"date-parts":[[2021,2,1]]},"published":{"date-parts":[[2020,7,27]]}}}