{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,1,3]],"date-time":"2024-01-03T06:00:51Z","timestamp":1704261651271},"reference-count":32,"publisher":"Oxford University Press (OUP)","issue":"18","license":[{"start":{"date-parts":[[2016,10,12]],"date-time":"2016-10-12T00:00:00Z","timestamp":1476230400000},"content-version":"vor","delay-in-days":145,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2016,9,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Functional protein\u2013protein interaction (PPI) networks elucidate molecular pathways underlying complex phenotypes, including those of human diseases. Extrapolation of domain\u2013domain interactions (DDIs) from known PPIs is a major domain-based method for inferring functional PPI networks. However, the protein domain is a functional unit of the protein. Therefore, we should be able to effectively infer functional interactions between proteins based on the co-occurrence of domains.<\/jats:p>\n               <jats:p>Results: Here, we present a method for inferring accurate functional PPIs based on the similarity of domain composition between proteins by weighted mutual information (MI) that assigned different weights to the domains based on their genome-wide frequencies. Weighted MI outperforms other domain-based network inference methods and is highly predictive for pathways as well as phenotypes. A genome-scale human functional network determined by our method reveals numerous communities that are significantly associated with known pathways and diseases. Domain-based functional networks may, therefore, have potential applications in mapping domain-to-pathway or domain-to-phenotype associations.<\/jats:p>\n               <jats:p>Availability and Implementation: Source code for calculating weighted mutual information based on the domain profile matrix is available from www.netbiolab.org\/w\/WMI.<\/jats:p>\n               <jats:p>Contact: \u00a0Insuklee@yonsei.ac.kr<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btw320","type":"journal-article","created":{"date-parts":[[2016,5,24]],"date-time":"2016-05-24T22:59:24Z","timestamp":1464130764000},"page":"2824-2830","source":"Crossref","is-referenced-by-count":15,"title":["Weighted mutual information analysis substantially improves domain-based functional network models"],"prefix":"10.1093","volume":"32","author":[{"given":"Jung Eun","family":"Shim","sequence":"first","affiliation":[{"name":"Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, Korea"}]},{"given":"Insuk","family":"Lee","sequence":"additional","affiliation":[{"name":"Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, Korea"}]}],"member":"286","published-online":{"date-parts":[[2016,5,20]]},"reference":[{"key":"2023020113390853800_btw320-B1","doi-asserted-by":"crossref","first-page":"D789","DOI":"10.1093\/nar\/gku1205","article-title":"OMIM.org: Online Mendelian Inheritance in Man (OMIM(R)), an online catalog of human genes and genetic disorders","volume":"43","author":"Amberger","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"2023020113390853800_btw320-B2","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":"Barabasi","year":"2011","journal-title":"Nat. Rev. Genet"},{"key":"2023020113390853800_btw320-B3","doi-asserted-by":"crossref","first-page":"bar068","DOI":"10.1093\/database\/bar068","article-title":"Manual GO annotation of predictive protein signatures: the InterPro approach to GO curation","volume":"2012","author":"Burge","year":"2012","journal-title":"Database"},{"key":"2023020113390853800_btw320-B4","doi-asserted-by":"crossref","first-page":"96","DOI":"10.1159\/000314272","article-title":"Metabolic syndrome in Cushing's syndrome","volume":"92","author":"Chanson","year":"2010","journal-title":"Neuroendocrinology"},{"key":"2023020113390853800_btw320-B5","doi-asserted-by":"crossref","first-page":"1701","DOI":"10.1126\/science.1085371","article-title":"Evolution of the protein repertoire","volume":"300","author":"Chothia","year":"2003","journal-title":"Science"},{"key":"2023020113390853800_btw320-B6","doi-asserted-by":"crossref","first-page":"1540","DOI":"10.1101\/gr.153002","article-title":"Inferring domain-domain interactions from protein-protein interactions","volume":"12","author":"Deng","year":"2002","journal-title":"Genome Res"},{"key":"2023020113390853800_btw320-B7","doi-asserted-by":"crossref","first-page":"160202","DOI":"10.1103\/PhysRevLett.94.160202","article-title":"Clique percolation in random networks","volume":"94","author":"Derenyi","year":"2005","journal-title":"Phys. Rev. Lett"},{"key":"2023020113390853800_btw320-B8","doi-asserted-by":"crossref","first-page":"D530","DOI":"10.1093\/nar\/gks1050","article-title":"Gene Ontology annotations and resources","volume":"41","author":"Gene Ontology Consortium","year":"2013","journal-title":"Nucleic Acids Res"},{"key":"2023020113390853800_btw320-B9","doi-asserted-by":"crossref","first-page":"368","DOI":"10.1016\/j.clinbiochem.2007.12.009","article-title":"Circulating P-, L- and E-selectins in Pseudoxanthoma elasticum patients","volume":"41","author":"Gotting","year":"2008","journal-title":"Clin. Biochem"},{"key":"2023020113390853800_btw320-B10","doi-asserted-by":"crossref","first-page":"125","DOI":"10.1007\/s00439-013-1377-1","article-title":"Network.assisted analysis to prioritize GWAS results: principles, methods and perspectives","volume":"133","author":"Jia","year":"2014","journal-title":"Hum. Genet"},{"key":"2023020113390853800_btw320-B11","doi-asserted-by":"crossref","first-page":"D1071","DOI":"10.1093\/nar\/gku1011","article-title":"Disease Ontology 2015 update: an expanded and updated database of human diseases for linking biomedical knowledge through disease data","volume":"43","author":"Kibbe","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"2023020113390853800_btw320-B12","doi-asserted-by":"crossref","first-page":"S9","DOI":"10.1186\/1477-5956-10-S1-S9","article-title":"IDDI: integrated domain-domain interaction and protein interaction analysis system","volume":"10","author":"Kim","year":"2012","journal-title":"Proteome Sci"},{"key":"2023020113390853800_btw320-B13","doi-asserted-by":"crossref","first-page":"690","DOI":"10.1016\/j.molcel.2015.05.008","article-title":"The cancer cell map initiative: defining the hallmark networks of cancer","volume":"58","author":"Krogan","year":"2015","journal-title":"Mol. Cell"},{"key":"2023020113390853800_btw320-B14","doi-asserted-by":"crossref","first-page":"1555","DOI":"10.1126\/science.1099511","article-title":"A probabilistic functional network of yeast genes","volume":"306","author":"Lee","year":"2004","journal-title":"Science"},{"key":"2023020113390853800_btw320-B15","doi-asserted-by":"crossref","first-page":"602","DOI":"10.1016\/j.gde.2013.09.003","article-title":"Network analysis of GWAS data","volume":"23","author":"Leiserson","year":"2013","journal-title":"Curr. Opin. Genet. Dev"},{"key":"2023020113390853800_btw320-B16","doi-asserted-by":"crossref","first-page":"R258","DOI":"10.1186\/gb-2007-8-12-r258","article-title":"Broad network-based predictability of Saccharomyces cerevisiae gene loss-of-function phenotypes","volume":"8","author":"McGary","year":"2007","journal-title":"Genome Biol"},{"key":"2023020113390853800_btw320-B17","doi-asserted-by":"crossref","first-page":"D213","DOI":"10.1093\/nar\/gku1243","article-title":"The InterPro protein families database: the classification resource after 15 years","volume":"43","author":"Mitchell","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"2023020113390853800_btw320-B18","doi-asserted-by":"crossref","first-page":"444","DOI":"10.1016\/j.tibs.2008.05.008","article-title":"Arrangements in the modular evolution of proteins","volume":"33","author":"Moore","year":"2008","journal-title":"Trends Biochem. Sci"},{"key":"2023020113390853800_btw320-B19","doi-asserted-by":"crossref","first-page":"615","DOI":"10.1038\/nmeth.3440","article-title":"Pathway and network analysis of cancer genomes","volume":"12","author":"The Mutation Consequences and Pathway Analysis working group of the International Cancer Genome Consortium","year":"2015","journal-title":"Nat. Methods"},{"key":"2023020113390853800_btw320-B20","doi-asserted-by":"crossref","first-page":"4590","DOI":"10.1118\/1.3463609","article-title":"Spatially weighted mutual information image registration for image guided radiation therapy","volume":"37","author":"Park","year":"2010","journal-title":"Med. Phys"},{"key":"2023020113390853800_btw320-B21","first-page":"6269","article-title":"Spatially weighted mutual information (SWMI) for registration of digitally reconstructed ex vivo whole mount histology and in vivo prostate MRI","volume":"2011","author":"Patel","year":"2011","journal-title":"Conf. Proc. IEEE Eng. Med. Biol. Soc"},{"key":"2023020113390853800_btw320-B22","doi-asserted-by":"crossref","first-page":"1359","DOI":"10.1002\/art.33487","article-title":"The loss of alpha2beta1 integrin suppresses joint inflammation and cartilage destruction in mouse models of rheumatoid arthritis","volume":"64","author":"Peters","year":"2012","journal-title":"Arthritis Rheum"},{"key":"2023020113390853800_btw320-B23","doi-asserted-by":"crossref","first-page":"147648","DOI":"10.1155\/2014\/147648","article-title":"Protein-protein interaction detection: methods and analysis","volume":"2014","author":"Rao","year":"2014","journal-title":"Int. J. Proteomics"},{"key":"2023020113390853800_btw320-B24","doi-asserted-by":"crossref","first-page":"2751","DOI":"10.1016\/j.febslet.2012.04.027","article-title":"Domain-mediated protein interaction prediction: From genome to network","volume":"586","author":"Reimand","year":"2012","journal-title":"FEBS Lett"},{"key":"2023020113390853800_btw320-B25","first-page":"91","article-title":"Self-similarity weighted mutual information: a new nonrigid image registration metric","volume":"15","author":"Rivaz","year":"2012","journal-title":"Med. Image Comput. Comput. Assist. Interv"},{"key":"2023020113390853800_btw320-B26","doi-asserted-by":"crossref","first-page":"231","DOI":"10.1080\/19768354.2015.1074108","article-title":"Network-assisted approaches for human disease research","volume":"19","author":"Shim","year":"2015","journal-title":"Anim. Cells Syst"},{"key":"2023020113390853800_btw320-B27","doi-asserted-by":"crossref","first-page":"681","DOI":"10.1006\/jmbi.2001.4920","article-title":"Correlated sequence-signatures as markers of protein\u2013protein interaction","volume":"311","author":"Sprinzak","year":"2001","journal-title":"J. Mol. Biol"},{"key":"2023020113390853800_btw320-B28","first-page":"25","article-title":"Serial nonrigid vascular registration using weighted normalized mutual information","volume":"2010","author":"Suh","year":"2010","journal-title":"Proc. IEEE Int. Symp. Biomed. Imaging"},{"key":"2023020113390853800_btw320-B29","doi-asserted-by":"crossref","first-page":"482","DOI":"10.1007\/PL00007887","article-title":"Relationship between anticoagulant medication and massive intraocular hemorrhage in age-related macular degeneration","volume":"238","author":"Tilanus","year":"2000","journal-title":"Graefes. Arch. Clin. Exp. Ophthalmol"},{"key":"2023020113390853800_btw320-B30","doi-asserted-by":"crossref","first-page":"S296","DOI":"10.1093\/bioinformatics\/17.suppl_1.S296","article-title":"Protein-protein interaction map inference using interacting domain profile pairs","volume":"17","author":"Wojcik","year":"2001","journal-title":"Bioinformatics"},{"key":"2023020113390853800_btw320-B31","doi-asserted-by":"crossref","first-page":"D730","DOI":"10.1093\/nar\/gkq1229","article-title":"DOMINE: a comprehensive collection of known and predicted domain-domain interactions","volume":"39","author":"Yellaboina","year":"2011","journal-title":"Nucleic Acids Res"},{"key":"2023020113390853800_btw320-B32","doi-asserted-by":"crossref","first-page":"1819","DOI":"10.1109\/TMI.2011.2150240","article-title":"A nonrigid registration framework using spatially encoded mutual information and free-form deformations","volume":"30","author":"Zhuang","year":"2011","journal-title":"IEEE Trans. Med. Imaging"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/32\/18\/2824\/49020719\/bioinformatics_32_18_2824.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/32\/18\/2824\/49020719\/bioinformatics_32_18_2824.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,1]],"date-time":"2023-02-01T23:43:50Z","timestamp":1675295030000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/32\/18\/2824\/1744011"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2016,5,20]]},"references-count":32,"journal-issue":{"issue":"18","published-print":{"date-parts":[[2016,9,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btw320","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2016,9,15]]},"published":{"date-parts":[[2016,5,20]]}}}