{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,23]],"date-time":"2025-10-23T16:38:07Z","timestamp":1761237487475},"reference-count":16,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":3240,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.0\/uk\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2008,1,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Proteins work together to drive biological processes in cellular machines. Summarizing global and local properties of the set of protein interactions, the interactome, is necessary for describing cellular systems. We consider a relatively simple per-protein feature of the interactome: the number of interaction partners for a protein, which in graph terminology is the degree of the protein.<\/jats:p>\n               <jats:p>Results: Using data subject to both stochastic and systematic sources of false positive and false negative observations, we develop an explicit probability model and resultant likelihood method to estimate node degree on portions of the interactome assayed by bait-prey technologies. This approach yields substantial improvement in degree estimation over the current practice that na\u00efvely sums observed edges. Accurate modeling of observed data in relation to true but unknown parameters of interest gives a formal point of reference from which to draw conclusions about the system under study.<\/jats:p>\n               <jats:p>Availability: All analyses discussed in this text can be performed using the ppiStats and ppiData packages available through the Bioconductor project (http:\/\/www.bioconductor.org).<\/jats:p>\n               <jats:p>Contact: \u00a0dscholtens@northwestern.edu<\/jats:p>\n               <jats:p>Supplementary information: Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btm565","type":"journal-article","created":{"date-parts":[[2007,11,20]],"date-time":"2007-11-20T01:13:06Z","timestamp":1195521186000},"page":"218-224","source":"Crossref","is-referenced-by-count":12,"title":["Estimating node degree in bait-prey graphs"],"prefix":"10.1093","volume":"24","author":[{"given":"Denise","family":"Scholtens","sequence":"first","affiliation":[{"name":"1 Department of Preventive Medicine, Northwestern University Medical School, 680 N. Lake Shore Drive Suite 1102, Chicago, IL 60611-4402, USA, 2EMBL Outstation \u2013 Hinxton, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK and 3Fred Hutchinson Cancer Research Center, Computational Biology Group, 1100 Fairview Avenue North \u2013 M2-B876, P.O. Box 19024, Seattle, Washington 98109-1024, USA"}]},{"given":"Tony","family":"Chiang","sequence":"additional","affiliation":[{"name":"1 Department of Preventive Medicine, Northwestern University Medical School, 680 N. Lake Shore Drive Suite 1102, Chicago, IL 60611-4402, USA, 2EMBL Outstation \u2013 Hinxton, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK and 3Fred Hutchinson Cancer Research Center, Computational Biology Group, 1100 Fairview Avenue North \u2013 M2-B876, P.O. Box 19024, Seattle, Washington 98109-1024, USA"}]},{"given":"Wolfgang","family":"Huber","sequence":"additional","affiliation":[{"name":"1 Department of Preventive Medicine, Northwestern University Medical School, 680 N. Lake Shore Drive Suite 1102, Chicago, IL 60611-4402, USA, 2EMBL Outstation \u2013 Hinxton, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK and 3Fred Hutchinson Cancer Research Center, Computational Biology Group, 1100 Fairview Avenue North \u2013 M2-B876, P.O. Box 19024, Seattle, Washington 98109-1024, USA"}]},{"given":"Robert","family":"Gentleman","sequence":"additional","affiliation":[{"name":"1 Department of Preventive Medicine, Northwestern University Medical School, 680 N. Lake Shore Drive Suite 1102, Chicago, IL 60611-4402, USA, 2EMBL Outstation \u2013 Hinxton, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK and 3Fred Hutchinson Cancer Research Center, Computational Biology Group, 1100 Fairview Avenue North \u2013 M2-B876, P.O. Box 19024, Seattle, Washington 98109-1024, USA"}]}],"member":"286","published-online":{"date-parts":[[2007,11,19]]},"reference":[{"key":"2023020209493011100_B1","doi-asserted-by":"crossref","first-page":"509","DOI":"10.1126\/science.286.5439.509","article-title":"Emergence of scaling in random networks","volume":"286","author":"Barab\u00e1si","year":"1999","journal-title":"Science"},{"key":"2023020209493011100_B2","doi-asserted-by":"crossref","first-page":"R186","DOI":"10.1186\/gb-2007-8-9-r186","article-title":"Coverage and error models of protein-protein interaction data by directed graph analysis","volume":"8","author":"Chiang","year":"2007","journal-title":"Genome Biol."},{"key":"2023020209493011100_B3","doi-asserted-by":"crossref","first-page":"439","DOI":"10.1074\/mcp.M600381-MCP200","article-title":"Toward a comprehensive atlas of the physical interactome of Saccharomyces cerevisiae","volume":"6","author":"Collins","year":"2007","journal-title":"Mol. Cell. 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