{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,8]],"date-time":"2026-09-08T13:43:11Z","timestamp":1788874991567,"version":"build-2803163510"},"reference-count":27,"publisher":"Oxford University Press (OUP)","issue":"12","license":[{"start":{"date-parts":[[2016,10,3]],"date-time":"2016-10-03T00:00:00Z","timestamp":1475452800000},"content-version":"vor","delay-in-days":845,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/3.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,6,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: While the manually curated Gene Ontology (GO) is widely used, inferring a GO directly from -omics data is a compelling new problem. Recognizing that ontologies are a directed acyclic graph (DAG) of terms and hierarchical relations, algorithms are needed that: analyze a full matrix of gene\u2013gene pairwise similarities from -omics data;infer true hierarchical structure in these data rather than enforcing hierarchy as a computational artifact; andrespect biological pleiotropy, by which a term in the hierarchy can relate to multiple higher level terms.<\/jats:p>\n               <jats:p>Methods addressing these requirements are just beginning to emerge\u2014none has been evaluated for GO inference.<\/jats:p>\n               <jats:p>Methods: We consider two algorithms [Clique Extracted Ontology (CliXO), LocalFitness] that uniquely satisfy these requirements, compared with methods including standard clustering. CliXO is a new approach that finds maximal cliques in a network induced by progressive thresholding of a similarity matrix. We evaluate each method\u2019s ability to reconstruct the GO biological process ontology from a similarity matrix based on (a) semantic similarities for GO itself or (b) three -omics datasets for yeast.<\/jats:p>\n               <jats:p>Results: For task (a) using semantic similarity, CliXO accurately reconstructs GO (&amp;gt;99% precision, recall) and outperforms other approaches (&amp;lt;20% precision, &amp;lt;20% recall). For task (b) using -omics data, CliXO outperforms other methods using two -omics datasets and achieves \u223c30% precision and recall using YeastNet v3, similar to an earlier approach (Network Extracted Ontology) and better than LocalFitness or standard clustering (20\u201325% precision, recall).<\/jats:p>\n               <jats:p>Conclusion: This study provides algorithmic foundation for building gene ontologies by capturing hierarchical and pleiotropic structure embedded in biomolecular data.<\/jats:p>\n               <jats:p>Contact: \u00a0tideker@ucsd.edu<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu282","type":"journal-article","created":{"date-parts":[[2014,6,16]],"date-time":"2014-06-16T21:55:09Z","timestamp":1402955709000},"page":"i34-i42","source":"Crossref","is-referenced-by-count":75,"title":["Inferring gene ontologies from pairwise similarity data"],"prefix":"10.1093","volume":"30","author":[{"given":"Michael","family":"Kramer","sequence":"first","affiliation":[{"name":"1 Department of Medicine and 2Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA 92093, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Janusz","family":"Dutkowski","sequence":"additional","affiliation":[{"name":"1 Department of Medicine and 2Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA 92093, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael","family":"Yu","sequence":"additional","affiliation":[{"name":"1 Department of Medicine and 2Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA 92093, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vineet","family":"Bafna","sequence":"additional","affiliation":[{"name":"1 Department of Medicine and 2Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA 92093, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Trey","family":"Ideker","sequence":"additional","affiliation":[{"name":"1 Department of Medicine and 2Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA 92093, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2014,6,11]]},"reference":[{"key":"2023012711104378500_btu282-B1","doi-asserted-by":"crossref","first-page":"761","DOI":"10.1038\/nature09182","article-title":"Link communities reveal multiscale complexity in networks","volume":"466","author":"Ahn","year":"2010","journal-title":"Nature"},{"key":"2023012711104378500_btu282-B2","doi-asserted-by":"crossref","first-page":"128","DOI":"10.1038\/nbt0210-128","article-title":"Ontology engineering","volume":"28","author":"Alterovitz","year":"2010","journal-title":"Nat. Biotechnol."},{"key":"2023012711104378500_btu282-B3","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":"2023012711104378500_btu282-B4","doi-asserted-by":"crossref","first-page":"84","DOI":"10.1093\/bioinformatics\/btr621","article-title":"Multifunctional proteins revealed by overlapping clustering in protein interaction network","volume":"28","author":"Becker","year":"2012","journal-title":"Bioinformatics"},{"key":"2023012711104378500_btu282-B27","doi-asserted-by":"crossref","first-page":"534","DOI":"10.1016\/j.cell.2014.03.009","article-title":"Siri of the cell: what biology could learn from the iPhone","volume":"157","author":"Carvunis","year":"2014","journal-title":"Cell"},{"key":"2023012711104378500_btu282-B5","doi-asserted-by":"crossref","first-page":"210","DOI":"10.1137\/0214017","article-title":"Arboricity and subgraph listing algorithms","volume":"14","author":"Chiba","year":"1985","journal-title":"SIAM J. Comput."},{"key":"2023012711104378500_btu282-B6","doi-asserted-by":"crossref","first-page":"425","DOI":"10.1126\/science.1180823","article-title":"The genetic landscape of a cell","volume":"327","author":"Costanzo","year":"2010","journal-title":"Science"},{"key":"2023012711104378500_btu282-B7","doi-asserted-by":"crossref","first-page":"34","DOI":"10.1038\/nbt.2476","article-title":"Automating the construction of gene ontologies","volume":"31","author":"Dolinski","year":"2013","journal-title":"Nat. Biotechnol."},{"key":"2023012711104378500_btu282-B8","doi-asserted-by":"crossref","first-page":"38","DOI":"10.1038\/nbt.2463","article-title":"A gene ontology inferred from molecular networks","volume":"31","author":"Dutkowski","year":"2013","journal-title":"Nat. Biotechnol."},{"key":"2023012711104378500_btu282-B9","doi-asserted-by":"crossref","first-page":"282","DOI":"10.4064\/cm-2-3-4-282-285","article-title":"Sur la liaison et la division des points d'un ensemble fini","volume":"2","author":"Florek","year":"1951","journal-title":"Colloq. Math."},{"key":"2023012711104378500_btu282-B10","doi-asserted-by":"crossref","first-page":"1425","DOI":"10.1101\/gr.180801","article-title":"Creating the gene ontology resource: design and implementation","volume":"11","author":"Gene Ontology Consortium","year":"2001","journal-title":"Genome Res."},{"key":"2023012711104378500_btu282-B11","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1016\/j.ajhg.2009.05.011","article-title":"Gene ontology analysis of GWA study data sets provides insights into the biology of bipolar disorder","volume":"85","author":"Holmans","year":"2009","journal-title":"Am. J. Hum. Genet."},{"key":"2023012711104378500_btu282-B12","doi-asserted-by":"crossref","first-page":"D898","DOI":"10.1093\/nar\/gkn786","article-title":"Implementation of GenePattern within the Stanford Microarray Database","volume":"37","author":"Hubble","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"2023012711104378500_btu282-B13","doi-asserted-by":"crossref","first-page":"D731","DOI":"10.1093\/nar\/gkt981","article-title":"YeastNet v3: a public database of data-specific and integrated functional gene networks for Saccharomyces cerevisiae","volume":"42","author":"Kim","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"2023012711104378500_btu282-B14","doi-asserted-by":"crossref","first-page":"e12528+","DOI":"10.1371\/journal.pone.0012528","article-title":"Community landscapes: an integrative approach to determine overlapping network module hierarchy, identify key nodes and predict network dynamics","volume":"5","author":"Kovacs","year":"2010","journal-title":"PLoS One"},{"key":"2023012711104378500_btu282-B15","doi-asserted-by":"crossref","first-page":"026109","DOI":"10.1103\/PhysRevE.78.026109","article-title":"Sequential algorithm for fast clique percolation","volume":"78","author":"Kumpula","year":"2008","journal-title":"Phys. Rev. E Stat. Nonlin. Soft Matter Phys."},{"key":"2023012711104378500_btu282-B16","doi-asserted-by":"crossref","first-page":"033015","DOI":"10.1088\/1367-2630\/11\/3\/033015","article-title":"Detecting the overlapping and hierarchical community structure in complex networks","volume":"11","author":"Lancichinetti","year":"2009","journal-title":"New J. Phys."},{"key":"2023012711104378500_btu282-B17","doi-asserted-by":"crossref","first-page":"S44","DOI":"10.1186\/1471-2105-12-S1-S44","article-title":"Resolving the structure of interactomes with hierarchical agglomerative clustering","volume":"12","author":"Park","year":"2011","journal-title":"BMC Bioinformatics"},{"key":"2023012711104378500_btu282-B18","doi-asserted-by":"crossref","first-page":"S2","DOI":"10.1186\/gb-2008-9-s1-s2","article-title":"A critical assessment of Mus musculus gene function prediction using integrated genomic evidence","volume":"9","author":"Pena-Castillo","year":"2008","journal-title":"Genome Biol."},{"key":"2023012711104378500_btu282-B19","first-page":"448","article-title":"Using information content to evaluate semantic similarity in a taxonomy","volume":"1","author":"Resnik","year":"1995","journal-title":"Int. Joint Conf. Artif."},{"key":"2023012711104378500_btu282-B20","doi-asserted-by":"crossref","first-page":"15224","DOI":"10.1073\/pnas.0703740104","article-title":"Extracting the hierarchical organization of complex systems","volume":"104","author":"Sales-Pardo","year":"2007","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023012711104378500_btu282-B21","volume-title":"Numerical Taxonomy. The Principles and Practice of Numerical Classification","author":"Sneath","year":"1973"},{"key":"2023012711104378500_btu282-B22","first-page":"1409","article-title":"A statistical method for evaluating systematic relationships","volume":"38","author":"Sokal","year":"1958","journal-title":"The University of Kansas Scientific Bulletin"},{"key":"2023012711104378500_btu282-B23","first-page":"1","article-title":"A method of establishing groups of equal amplitude in plant sociology based on similarity of species and its application to analyses of the vegetation on Danish commons","volume":"5","author":"S\u00f8rensen","year":"1948","journal-title":"Biol. Skr."},{"key":"2023012711104378500_btu282-B24","doi-asserted-by":"crossref","first-page":"843","DOI":"10.1038\/nrg2884","article-title":"Analysing biological pathways in genome-wide association studies","volume":"11","author":"Wang","year":"2010","journal-title":"Nat. Rev. Genet."},{"key":"2023012711104378500_btu282-B25","doi-asserted-by":"crossref","first-page":"236","DOI":"10.1080\/01621459.1963.10500845","article-title":"Hierarchical grouping to optimize an objective function","volume":"58","author":"Ward","year":"1963","journal-title":"J. Am. Stat. Assoc."},{"key":"2023012711104378500_btu282-B26","doi-asserted-by":"crossref","first-page":"e12139","DOI":"10.1371\/journal.pone.0012139","article-title":"A genome-wide gene function prediction resource for Drosophila melanogaster","volume":"5","author":"Yan","year":"2010","journal-title":"PLoS One"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/30\/12\/i34\/48927108\/bioinformatics_30_12_i34.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/30\/12\/i34\/48927108\/bioinformatics_30_12_i34.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,27]],"date-time":"2023-01-27T11:50:38Z","timestamp":1674820238000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/30\/12\/i34\/389066"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2014,6,11]]},"references-count":27,"journal-issue":{"issue":"12","published-print":{"date-parts":[[2014,6,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btu282","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2014,6,15]]},"published":{"date-parts":[[2014,6,11]]}}}