{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:34:07Z","timestamp":1772138047061,"version":"3.50.1"},"reference-count":35,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2021,12,16]],"date-time":"2021-12-16T00:00:00Z","timestamp":1639612800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"MEXT Program for Promoting Researches on the super computer Fugaku"},{"name":"JSPS KAKENHI","award":["JP18H04899"],"award-info":[{"award-number":["JP18H04899"]}]},{"name":"JSPS KAKENHI","award":["JP18K18151"],"award-info":[{"award-number":["JP18K18151"]}]},{"name":"JSPS KAKENHI","award":["JP20H04282"],"award-info":[{"award-number":["JP20H04282"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,2,7]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>The full spectrum of abnormalities in cancer-associated protein complexes remains largely unknown. Comparing the co-expression structure of each protein complex between tumor and healthy cells may provide insights regarding cancer-specific protein dysfunction. However, the technical limitations of mass spectrometry-based proteomics, including contamination with biological protein variants, causes noise that leads to non-negligible over- (or under-) estimating co-expression.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We propose a robust algorithm for identifying protein complex aberrations in cancer based on differential protein co-expression testing. Our method based on a copula is sufficient for improving identification accuracy with noisy data compared to conventional linear correlation-based approaches. As an application, we use large-scale proteomic data from renal cancer to show that important protein complexes, regulatory signaling pathways and drug targets can be identified. The proposed approach surpasses traditional linear correlations to provide insights into higher-order differential co-expression structures.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>https:\/\/github.com\/ymatts\/RoDiCE.<\/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\/btab612","type":"journal-article","created":{"date-parts":[[2021,9,8]],"date-time":"2021-09-08T07:46:10Z","timestamp":1631087170000},"page":"1269-1276","source":"Crossref","is-referenced-by-count":2,"title":["RoDiCE: robust differential protein co-expression analysis for cancer complexome"],"prefix":"10.1093","volume":"38","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3977-4313","authenticated-orcid":false,"given":"Yusuke","family":"Matsui","sequence":"first","affiliation":[{"name":"Biomedical and Health Informatics Unit, Department of Integrated Health Science, Nagoya University Graduate School of Medicine , 461-8673 Nagoya, Aichi, Japan"},{"name":"Institute for Glyco-core Research (iGCORE), Nagoya University , 461-8673 Nagoya, Aichi, Japan"}]},{"given":"Yuichi","family":"Abe","sequence":"additional","affiliation":[{"name":"Division of Molecular Diagnostics, Aichi Cancer Center Research Institute , 464-0021 Nagoya, Aichi, Japan"}]},{"given":"Kohei","family":"Uno","sequence":"additional","affiliation":[{"name":"Biomedical and Health Informatics Unit, Department of Integrated Health Science, Nagoya University Graduate School of Medicine , 461-8673 Nagoya, Aichi, Japan"}]},{"given":"Satoru","family":"Miyano","sequence":"additional","affiliation":[{"name":"Department of Integrated Data Science, M&D Data Science Center, Tokyo Medical and Dental University , 113-8510 Tokyo, Japan"}]}],"member":"286","published-online":{"date-parts":[[2021,12,16]]},"reference":[{"key":"2023020108544226000_btab612-B1","doi-asserted-by":"crossref","first-page":"1021","DOI":"10.1093\/bioinformatics\/btl039","article-title":"CFinder: locating cliques and overlapping modules in biological networks","volume":"22","author":"Adamcsek","year":"2006","journal-title":"Bioinformatics"},{"key":"2023020108544226000_btab612-B2","author":"Allaire","year":"2019"},{"key":"2023020108544226000_btab612-B3","doi-asserted-by":"crossref","first-page":"e1002955","DOI":"10.1371\/journal.pcbi.1002955","article-title":"Dissection of regulatory networks that are altered in disease via differential co-expression","volume":"9","author":"Amar","year":"2013","journal-title":"PLoS Comput. 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