{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,23]],"date-time":"2025-10-23T16:36:46Z","timestamp":1761237406806,"version":"3.32.0"},"reference-count":27,"publisher":"Oxford University Press (OUP)","issue":"5","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2007,3,1]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Motivation: Large-scale mappings of protein\u2013protein interactions have started to give us new views of the complex molecular mechanisms inside a cell. After initial projects to systematically map protein interactions in model organisms such as yeast, worm and fly, researchers have begun to focus on the mapping of the human interactome. To tackle this enormous challenge, different approaches have been proposed and pursued. While several large-scale human protein interaction maps have recently been published, their quality remains to be critically assessed.<\/jats:p><jats:p>Results: We present here a first comparative analysis of eight currently available large-scale maps with a total of over 10\u2009000 unique proteins and 57\u2009000 interactions included. They are based either on literature search, orthology or by yeast-two-hybrid assays. Comparison reveals only a small, but statistically significant overlap. More importantly, our analysis gives clear indications that all interaction maps imply considerable selection and detection biases. These results have to be taken into account for future assembly of the human interactome.<\/jats:p><jats:p>Availability: An integrated human interaction network called Unified Human Interactome (UniHI) is made publicly accessible at http:\/\/www.mdc-berlin.de\/unihi.<\/jats:p><jats:p>Contact: \u00a0m.futschik@biologie.hu-berlin.de<\/jats:p><jats:p>Supplementary information: Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btl683","type":"journal-article","created":{"date-parts":[[2007,1,20]],"date-time":"2007-01-20T01:12:50Z","timestamp":1169255570000},"page":"605-611","source":"Crossref","is-referenced-by-count":66,"title":["Comparison of human protein\u2013protein interaction maps"],"prefix":"10.1093","volume":"23","author":[{"given":"Matthias E.","family":"Futschik","sequence":"first","affiliation":[{"name":"1 Institute for Theoretical Biology, Charit\u00e9, Humboldt-Universit\u00e4t and 2Max-Delbr\u00fcck-Centrum, Invalidenstrasse 43, 10115 Berlin, Germany"}]},{"given":"Gautam","family":"Chaurasia","sequence":"additional","affiliation":[{"name":"1 Institute for Theoretical Biology, Charit\u00e9, Humboldt-Universit\u00e4t and 2Max-Delbr\u00fcck-Centrum, Invalidenstrasse 43, 10115 Berlin, Germany"},{"name":"1 Institute for Theoretical Biology, Charit\u00e9, Humboldt-Universit\u00e4t and 2Max-Delbr\u00fcck-Centrum, Invalidenstrasse 43, 10115 Berlin, Germany"}]},{"given":"Hanspeter","family":"Herzel","sequence":"additional","affiliation":[{"name":"1 Institute for Theoretical Biology, Charit\u00e9, Humboldt-Universit\u00e4t and 2Max-Delbr\u00fcck-Centrum, Invalidenstrasse 43, 10115 Berlin, Germany"}]}],"member":"286","published-online":{"date-parts":[[2007,1,19]]},"reference":[{"key":"2023041109374806500_","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1038\/75556","article-title":"Gene ontology: tool for the unification of biology. The Gene Ontology Consortium","volume":"25","author":"Ashburner","year":"2000","journal-title":"Nat. Genet."},{"key":"2023041109374806500_","doi-asserted-by":"crossref","first-page":"991","DOI":"10.1038\/nbt1002-991","article-title":"Analyzing yeast protein-protein interaction data obtained from different sources","volume":"20","author":"Bader","year":"2002","journal-title":"Nat. Biotechnol."},{"key":"2023041109374806500_","doi-asserted-by":"crossref","first-page":"242","DOI":"10.1093\/nar\/29.1.242","article-title":"BIND \u2013 The biomolecular interaction network database","volume":"29","author":"Bader","year":"2001","journal-title":"Nucleic Acids Res."},{"key":"2023041109374806500_","doi-asserted-by":"crossref","first-page":"3353","DOI":"10.1093\/bioinformatics\/bth405","article-title":"A graph-theoretic approach to testing associations between disparate sources of functional genomics data","volume":"20","author":"Balasubramanian","year":"2004","journal-title":"Bioinformatics"},{"key":"2023041109374806500_","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1111\/j.2517-6161.1995.tb02031.x","article-title":"Controlling the false discovery rate \u2013 a practical and powerful approach to multiple testing","volume":"57","author":"Benjamini","year":"1995","journal-title":"J. Roy. Stat. Soc. B"},{"key":"2023041109374806500_","doi-asserted-by":"crossref","first-page":"292","DOI":"10.1016\/j.sbi.2004.05.003","article-title":"Protein interaction networks from yeast to human","volume":"14","author":"Bork","year":"2004","journal-title":"Curr. Opin. Struct. Biol."},{"key":"2023041109374806500_","doi-asserted-by":"crossref","first-page":"2076","DOI":"10.1093\/bioinformatics\/bti273","article-title":"Online predicted human interaction database","volume":"21","author":"Brown","year":"2005","journal-title":"Bioinformatics"},{"key":"2023041109374806500_","doi-asserted-by":"crossref","first-page":"135","DOI":"10.1093\/bioinformatics\/bth458","article-title":"Network structures and algorithms in Bioconductor","volume":"21","author":"Carey","year":"2005","journal-title":"Bioinformatics"},{"key":"2023041109374806500_","doi-asserted-by":"crossref","first-page":"D590","DOI":"10.1093\/nar\/gkl817","article-title":"UniHI: an entry gate to the human protein interactome","volume":"35","author":"Chaurasia","year":"2007","journal-title":"Nucleic Acids Res."},{"key":"2023041109374806500_","doi-asserted-by":"crossref","first-page":"141","DOI":"10.1038\/415141a","article-title":"Functional organization of the yeast proteome by systematic analysis of protein complexes","volume":"415","author":"Gavin","year":"2002","journal-title":"Nature"},{"key":"2023041109374806500_","doi-asserted-by":"crossref","first-page":"R80","DOI":"10.1186\/gb-2004-5-10-r80","article-title":"Bioconductor: open software development for computational biology and bioinformatics","volume":"5","author":"Gentleman","year":"2004","journal-title":"Genome Biol."},{"key":"2023041109374806500_","doi-asserted-by":"crossref","first-page":"1727","DOI":"10.1126\/science.1090289","article-title":"A protein interaction map of Drosophila melanogaster","volume":"302","author":"Giot","year":"2003","journal-title":"Science"},{"key":"2023041109374806500_","doi-asserted-by":"crossref","first-page":"853","DOI":"10.1016\/j.molcel.2004.09.016","article-title":"A protein interaction network links GIT1, an enhancer of huntingtin aggregation, to Huntington's disease","volume":"15","author":"Goehler","year":"2004","journal-title":"Mol. Cell"},{"key":"2023041109374806500_","doi-asserted-by":"crossref","first-page":"4569","DOI":"10.1073\/pnas.061034498","article-title":"A comprehensive two-hybrid analysis to explore the yeast protein interactome","volume":"98","author":"Ito","year":"2001","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"2023041109374806500_","doi-asserted-by":"crossref","first-page":"449","DOI":"10.1126\/science.1087361","article-title":"A Bayesian networks approach for predicting protein-protein interactions from genomic data","volume":"302","author":"Jansen","year":"2003","journal-title":"Science"},{"key":"2023041109374806500_","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":"2023041109374806500_","doi-asserted-by":"crossref","first-page":"R63","DOI":"10.1186\/gb-2004-5-9-r63","article-title":"A first-draft human protein-interaction map","volume":"5","author":"Lehner","year":"2004","journal-title":"Genome Biol."},{"key":"2023041109374806500_","doi-asserted-by":"crossref","first-page":"540","DOI":"10.1126\/science.1091403","article-title":"A map of the interactome network of the metazoan C. elegans","volume":"303","author":"Li","year":"2004","journal-title":"Science"},{"key":"2023041109374806500_","doi-asserted-by":"crossref","first-page":"2363","DOI":"10.1101\/gr.1680803","article-title":"Development of human protein reference database as an initial platform for approaching systems biology in humans","volume":"13","author":"Peri","year":"2003","journal-title":"Genome Res."},{"key":"2023041109374806500_","doi-asserted-by":"crossref","first-page":"S21","DOI":"10.1186\/1471-2105-6-S4-S21","article-title":"HomoMINT: an inferred human network based on orthology mapping of protein interactions discovered in model organisms","volume":"6","author":"Persico","year":"2005","journal-title":"BMC Bioinformatics"},{"key":"2023041109374806500_","doi-asserted-by":"crossref","first-page":"R40","DOI":"10.1186\/gb-2005-6-5-r40","article-title":"Consolidating the set of known human protein-protein interactions in preparation for large-scale mapping of the human interactome","volume":"6","author":"Ramani","year":"2005","journal-title":"Genome Biol."},{"key":"2023041109374806500_","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1186\/jbiol36","article-title":"Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae","volume":"5","author":"Reguly","year":"2006","journal-title":"J. Biol."},{"key":"2023041109374806500_","doi-asserted-by":"crossref","first-page":"1173","DOI":"10.1038\/nature04209","article-title":"Towards a proteome-scale map of the human protein-protein interaction network","volume":"437","author":"Rual","year":"2005","journal-title":"Nature"},{"key":"2023041109374806500_","doi-asserted-by":"crossref","first-page":"1257","DOI":"10.1038\/82360","article-title":"A network of protein-protein interactions in yeast","volume":"18","author":"Schwikowski","year":"2000","journal-title":"Nat. Biotechnol."},{"key":"2023041109374806500_","doi-asserted-by":"crossref","first-page":"957","DOI":"10.1016\/j.cell.2005.08.029","article-title":"A human protein-protein interaction network: a resource for annotating the proteome","volume":"122","author":"Stelzl","year":"2005","journal-title":"Cell"},{"key":"2023041109374806500_","doi-asserted-by":"crossref","first-page":"623","DOI":"10.1038\/35001009","article-title":"A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae","volume":"403","author":"Uetz","year":"2000","journal-title":"Nature"},{"key":"2023041109374806500_","doi-asserted-by":"crossref","first-page":"399","DOI":"10.1038\/nature750","article-title":"Comparative assessment of large-scale data sets of protein-protein interactions","volume":"417","author":"von Mering","year":"2002","journal-title":"Nature"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/23\/5\/605\/49829648\/bioinformatics_23_5_605.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/23\/5\/605\/49829648\/bioinformatics_23_5_605.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,1,13]],"date-time":"2025-01-13T03:04:52Z","timestamp":1736737492000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/23\/5\/605\/239354"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2007,1,19]]},"references-count":27,"journal-issue":{"issue":"5","published-print":{"date-parts":[[2007,3,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btl683","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"type":"electronic","value":"1367-4811"},{"type":"print","value":"1367-4803"}],"subject":[],"published-other":{"date-parts":[[2007,3]]},"published":{"date-parts":[[2007,1,19]]}}}