{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,8,23]],"date-time":"2024-08-23T15:51:17Z","timestamp":1724428277487},"reference-count":57,"publisher":"Oxford University Press (OUP)","issue":"13","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":1937,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.5"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2011,7,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Quantitative experimental analyses of the nuclear interior reveal a morphologically structured yet dynamic mix of membraneless compartments. Major nuclear events depend on the functional integrity and timely assembly of these intra-nuclear compartments. Yet, unknown drivers of protein mobility ensure that they are in the right place at the time when they are needed.<\/jats:p>\n               <jats:p>Results: This study investigates determinants of associations between eight intra-nuclear compartments and their proteins in heterogeneous genome-wide data. We develop a model based on a range of candidate determinants, capable of mapping the intra-nuclear organization of proteins. The model integrates protein interactions, protein domains, post-translational modification sites and protein sequence data. The predictions of our model are accurate with a mean AUC (over all compartments) of 0.71.<\/jats:p>\n               <jats:p>We present a complete map of the association of 3567 mouse nuclear proteins with intra-nuclear compartments. Each decision is explained in terms of essential interactions and domains, and qualified with a false discovery assessment. Using this resource, we uncover the collective role of transcription factors in each of the compartments. We create diagrams illustrating the outcomes of a Gene Ontology enrichment analysis. Associated with an extensive range of transcription factors, the analysis suggests that PML bodies coordinate regulatory immune responses.<\/jats:p>\n               <jats:p>Contact: \u00a0m.boden@uq.edu.au<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btr217","type":"journal-article","created":{"date-parts":[[2011,6,17]],"date-time":"2011-06-17T23:32:32Z","timestamp":1308353552000},"page":"i7-i14","source":"Crossref","is-referenced-by-count":16,"title":["Sorting the nuclear proteome"],"prefix":"10.1093","volume":"27","author":[{"given":"Denis C.","family":"Bauer","sequence":"first","affiliation":[{"name":"1 Queensland Brain Institute, 2Institute for Molecular Bioscience, 3School of Chemistry and Molecular Biosciences, 4Queensland Facility for Advanced Bioinformatics, The University of Queensland, St Lucia, Australia, 5Departments of Pathology and Biochemistry & Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada and 6School of Information Technology and Electrical Engineering, The University of Queensland, St Lucia, Australia"},{"name":"1 Queensland Brain Institute, 2Institute for Molecular Bioscience, 3School of Chemistry and Molecular Biosciences, 4Queensland Facility for Advanced Bioinformatics, The University of Queensland, St Lucia, Australia, 5Departments of Pathology and Biochemistry & Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada and 6School of Information Technology and Electrical Engineering, The University of Queensland, St Lucia, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kai","family":"Willadsen","sequence":"additional","affiliation":[{"name":"1 Queensland Brain Institute, 2Institute for Molecular Bioscience, 3School of Chemistry and Molecular Biosciences, 4Queensland Facility for Advanced Bioinformatics, The University of Queensland, St Lucia, Australia, 5Departments of Pathology and Biochemistry & Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada and 6School of Information Technology and Electrical Engineering, The University of Queensland, St Lucia, Australia"},{"name":"1 Queensland Brain Institute, 2Institute for Molecular Bioscience, 3School of Chemistry and Molecular Biosciences, 4Queensland Facility for Advanced Bioinformatics, The University of Queensland, St Lucia, Australia, 5Departments of Pathology and Biochemistry & Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada and 6School of Information Technology and Electrical Engineering, The University of Queensland, St Lucia, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Fabian A.","family":"Buske","sequence":"additional","affiliation":[{"name":"1 Queensland Brain Institute, 2Institute for Molecular Bioscience, 3School of Chemistry and Molecular Biosciences, 4Queensland Facility for Advanced Bioinformatics, The University of Queensland, St Lucia, Australia, 5Departments of Pathology and Biochemistry & Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada and 6School of Information Technology and Electrical Engineering, The University of Queensland, St Lucia, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kim-Anh","family":"L\u00ea Cao","sequence":"additional","affiliation":[{"name":"1 Queensland Brain Institute, 2Institute for Molecular Bioscience, 3School of Chemistry and Molecular Biosciences, 4Queensland Facility for Advanced Bioinformatics, The University of Queensland, St Lucia, Australia, 5Departments of Pathology and Biochemistry & Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada and 6School of Information Technology and Electrical Engineering, The University of Queensland, St Lucia, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Timothy L.","family":"Bailey","sequence":"additional","affiliation":[{"name":"1 Queensland Brain Institute, 2Institute for Molecular Bioscience, 3School of Chemistry and Molecular Biosciences, 4Queensland Facility for Advanced Bioinformatics, The University of Queensland, St Lucia, Australia, 5Departments of Pathology and Biochemistry & Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada and 6School of Information Technology and Electrical Engineering, The University of Queensland, St Lucia, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Graham","family":"Dellaire","sequence":"additional","affiliation":[{"name":"1 Queensland Brain Institute, 2Institute for Molecular Bioscience, 3School of Chemistry and Molecular Biosciences, 4Queensland Facility for Advanced Bioinformatics, The University of Queensland, St Lucia, Australia, 5Departments of Pathology and Biochemistry & Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada and 6School of Information Technology and Electrical Engineering, The University of Queensland, St Lucia, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mikael","family":"Bod\u00e9n","sequence":"additional","affiliation":[{"name":"1 Queensland Brain Institute, 2Institute for Molecular Bioscience, 3School of Chemistry and Molecular Biosciences, 4Queensland Facility for Advanced Bioinformatics, The University of Queensland, St Lucia, Australia, 5Departments of Pathology and Biochemistry & Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada and 6School of Information Technology and Electrical Engineering, The University of Queensland, St Lucia, Australia"},{"name":"1 Queensland Brain Institute, 2Institute for Molecular Bioscience, 3School of Chemistry and Molecular Biosciences, 4Queensland Facility for Advanced Bioinformatics, The University of Queensland, St Lucia, Australia, 5Departments of Pathology and Biochemistry & Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada and 6School of Information Technology and Electrical Engineering, The University of Queensland, St Lucia, Australia"},{"name":"1 Queensland Brain Institute, 2Institute for Molecular Bioscience, 3School of Chemistry and Molecular Biosciences, 4Queensland Facility for Advanced Bioinformatics, The University of Queensland, St Lucia, Australia, 5Departments of Pathology and Biochemistry & Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada and 6School of Information Technology and Electrical Engineering, The University of Queensland, St Lucia, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2011,6,14]]},"reference":[{"key":"2023012512155584500_B1","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/S0960-9822(01)00650-9","article-title":"Directed proteomic analysis of the human 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USA"},{"key":"2023012512155584500_B5","doi-asserted-by":"crossref","first-page":"1006","DOI":"10.1038\/nrm2277","article-title":"Structure, dynamics and functions of promyelocytic leukaemia nuclear bodies","volume":"8","author":"Bernardi","year":"2007","journal-title":"Nat. Rev. Mol. 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Cell Biol."},{"key":"2023012512155584500_B9","doi-asserted-by":"crossref","first-page":"291","DOI":"10.1089\/cmb.2007.0163","article-title":"Determining nucleolar association from sequence by leveraging protein-protein interactions","volume":"15","author":"Bod\u00e9n","year":"2008","journal-title":"J. Comput. Biol."},{"key":"2023012512155584500_B10","doi-asserted-by":"crossref","first-page":"617","DOI":"10.1089\/cmb.2009.0140","article-title":"A Bayesian network model of proteins' association with Promyelocytic leukemia (PML) nuclear bodies","volume":"17","author":"Bod\u00e9n","year":"2010","journal-title":"J. Comput. Biol."},{"key":"2023012512155584500_B11","doi-asserted-by":"crossref","first-page":"283","DOI":"10.1083\/jcb.148.2.283","article-title":"Promyelocytic leukemia (PML) nuclear bodies are protein structures that do not accumulate RNA","volume":"148","author":"Boisvert","year":"2000","journal-title":"J. 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