{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,9,19]],"date-time":"2025-09-19T09:24:10Z","timestamp":1758273850068},"reference-count":32,"publisher":"Oxford University Press (OUP)","issue":"7","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2009,4,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Modules in biology appeared quickly as an accurate way for summarizing complex living systems by simple ones. Therefore, finding an appropriate relationship between modules extracted from a biological graph and protein complexes remains a crucial task. Recent studies successfully proposed various descriptions of protein interaction networks. These approaches succeed in showing modules within the network and how the modules interact. However, describing the interactions within the modules, i.e. intra-modular interactions, remains little analyzed despite its interest for understanding module functions.<\/jats:p>\n               <jats:p>Results: We overcome this weakness by adding a complementary description to the already successful approaches: a hierarchical decomposition named homogeneous decomposition. This decomposition represents a natural refinement of previous analyses and details interactions within a module. We propose to illustrate these improvements by three practical cases. Among them, we decompose the yeast protein interaction network and show reachable biological insights that might be extracted from a complex large-scale network.<\/jats:p>\n               <jats:p>Availability: A program is at disposal under CeCILL license at: www.lina.univ-nantes.fr\/combi\/DH\/Home.html<\/jats:p>\n               <jats:p>Contact: \u00a0irena.rusu@univ-nantes.fr<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btp083","type":"journal-article","created":{"date-parts":[[2009,2,18]],"date-time":"2009-02-18T03:25:13Z","timestamp":1234927513000},"page":"926-932","source":"Crossref","is-referenced-by-count":3,"title":["Homogeneous decomposition of protein interaction networks: refining the description of intra-modular interactions"],"prefix":"10.1093","volume":"25","author":[{"given":"G\u00e9raldine","family":"Del Mondo","sequence":"first","affiliation":[{"name":"Computational Biology group (ComBi) - LINA, Universit\u00e9 de Nantes, CNRS UMR 6241, 2 rue de la Houssini\u00e8re, 44300 Nantes, France"}]},{"given":"Damien","family":"Eveillard","sequence":"additional","affiliation":[{"name":"Computational Biology group (ComBi) - LINA, Universit\u00e9 de Nantes, CNRS UMR 6241, 2 rue de la Houssini\u00e8re, 44300 Nantes, France"}]},{"given":"Irena","family":"Rusu","sequence":"additional","affiliation":[{"name":"Computational Biology group (ComBi) - LINA, Universit\u00e9 de Nantes, CNRS UMR 6241, 2 rue de la Houssini\u00e8re, 44300 Nantes, France"}]}],"member":"286","published-online":{"date-parts":[[2009,2,17]]},"reference":[{"key":"2023013110163438300_B1","article-title":"A linear algorithm for the homogeneous decomposition of graphs","volume-title":"Technical Report M-9615","author":"Baumann","year":"1996"},{"key":"2023013110163438300_B2","doi-asserted-by":"crossref","first-page":"3710","DOI":"10.1093\/bioinformatics\/bth456","article-title":"GO::TermFinder\u2013open source software for accessing gene ontology information and finding significantly enriched gene ontology terms associated with a list of genes","volume":"20","author":"Boyle","year":"2004","journal-title":"Bioinformatics"},{"key":"2023013110163438300_B3","doi-asserted-by":"crossref","first-page":"1950","DOI":"10.1073\/pnas.91.5.1950","article-title":"A multisubunit complex containing the SWI1\/ADR6, SWI2\/SNF2, SWI3, SNF5, and SNF6 gene products isolated from yeast","volume":"91","author":"Cairns","year":"1994","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023013110163438300_B4","doi-asserted-by":"crossref","first-page":"1249","DOI":"10.1016\/S0092-8674(00)81820-6","article-title":"RSC, an essential, abundant chromatin-remodeling complex","volume":"87","author":"Cairns","year":"1996","journal-title":"Cell"},{"key":"2023013110163438300_B5","doi-asserted-by":"crossref","first-page":"326","DOI":"10.1016\/j.ceb.2007.04.009","article-title":"Nuclear actin and actin-related proteins in chromatin dynamics","volume":"19","author":"Chen","year":"2007","journal-title":"Curr. Opin. Cell Biol."},{"key":"2023013110163438300_B6","doi-asserted-by":"crossref","first-page":"1575","DOI":"10.1093\/nar\/30.7.1575","article-title":"An efficient algorithm for large-scale detection of protein families","volume":"30","author":"Enright","year":"2002","journal-title":"Nucleic Acids Res."},{"key":"2023013110163438300_B7","doi-asserted-by":"crossref","first-page":"R57","DOI":"10.1186\/gb-2004-5-8-r57","article-title":"Modular decomposition of protein-protein interaction networks","volume":"5","author":"Gagneur","year":"2004","journal-title":"Genome Biol."},{"key":"2023013110163438300_B8","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":"2023013110163438300_B9","doi-asserted-by":"crossref","first-page":"631","DOI":"10.1038\/nature04532","article-title":"Proteome survey reveals modularity of the yeast cell machinery","volume":"440","author":"Gavin","year":"2006","journal-title":"Nature"},{"key":"2023013110163438300_B10","doi-asserted-by":"crossref","first-page":"387","DOI":"10.1038\/nature00935","article-title":"Functional profiling of the Saccharomyces cerevisiae genome","volume":"418","author":"Giaever","year":"2002","journal-title":"Nature"},{"key":"2023013110163438300_B11","doi-asserted-by":"crossref","first-page":"025101","DOI":"10.1103\/PhysRevE.70.025101","article-title":"Modularity from fluctuations in random graphs and complex networks","volume":"70","author":"Guimer\u00e0","year":"2004","journal-title":"Phys. Rev. E. Stat. Nonlin. Soft Matter phys."},{"key":"2023013110163438300_B12","doi-asserted-by":"crossref","first-page":"201","DOI":"10.1016\/0166-218X(79)90043-X","article-title":"On the X-join decomposition for undirected graphs","volume":"1","author":"Habib","year":"1979","journal-title":"Discrete Appl. Math."},{"key":"2023013110163438300_B13","doi-asserted-by":"crossref","first-page":"120","DOI":"10.1186\/gb-2006-7-11-120","article-title":"How complete are current yeast and human protein-interaction networks?","volume":"7","author":"Hart","year":"2006","journal-title":"Genome Biol."},{"key":"2023013110163438300_B14","doi-asserted-by":"crossref","first-page":"236","DOI":"10.1186\/1471-2105-8-236","article-title":"A high-accuracy consensus map of yeast protein complexes reveals modular nature of gene essentiality","volume":"8","author":"Hart","year":"2007","journal-title":"BMC Bioinformatics"},{"issue":"Suppl. 6761","key":"2023013110163438300_B15","doi-asserted-by":"crossref","first-page":"C47","DOI":"10.1038\/35011540","article-title":"From molecular to modular cell biology","volume":"402","author":"Hartwell","year":"1999","journal-title":"Nature"},{"key":"2023013110163438300_B16","doi-asserted-by":"crossref","first-page":"e88","DOI":"10.1371\/journal.pgen.0020088","article-title":"Why do hubs tend to be essential in protein networks?","volume":"2","author":"He","year":"2006","journal-title":"PLoS Genet."},{"key":"2023013110163438300_B17","doi-asserted-by":"crossref","first-page":"2868","DOI":"10.1101\/gad.8.23.2868","article-title":"TFIIF-TAF-RNA polymerase II connection","volume":"8","author":"Henry","year":"1994","journal-title":"Genes Dev."},{"key":"2023013110163438300_B18","doi-asserted-by":"crossref","first-page":"180","DOI":"10.1038\/415180a","article-title":"Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry","volume":"415","author":"Ho","year":"2002","journal-title":"Nature"},{"key":"2023013110163438300_B19","doi-asserted-by":"crossref","first-page":"448","DOI":"10.1137\/S0895480191196812","article-title":"P-components and the homogeneous decomposition of graphs","volume":"8","author":"Jamison","year":"1995","journal-title":"SIAM J. Discrete Math."},{"key":"2023013110163438300_B20","doi-asserted-by":"crossref","first-page":"651","DOI":"10.1038\/35036627","article-title":"The large-scale organization of metabolic networks","volume":"407","author":"Jeong","year":"2000","journal-title":"Nature"},{"key":"2023013110163438300_B21","doi-asserted-by":"crossref","first-page":"398","DOI":"10.1016\/j.bbrc.2005.04.158","article-title":"Anc1 interacts with the catalytic subunits of the general transcription factors TFIID and TFIIF, the chromatin remodeling complexes RSC and INO80, and the histone acetyltransferase complex NuA3","volume":"332","author":"Kabani","year":"2005","journal-title":"Biochem. Biophys. Res. Commun."},{"key":"2023013110163438300_B22","doi-asserted-by":"crossref","first-page":"599","DOI":"10.1016\/0092-8674(94)90221-6","article-title":"A multiprotein mediator of transcriptional activation and its interaction with the C-terminal repeat domain of RNA polymerase II","volume":"77","author":"Kim","year":"1994","journal-title":"Cell"},{"key":"2023013110163438300_B23","doi-asserted-by":"crossref","first-page":"637","DOI":"10.1038\/nature04670","article-title":"Global landscape of protein complexes in the yeast saccharomyces cerevisiae","volume":"440","author":"Krogan","year":"2006","journal-title":"Nature"},{"key":"2023013110163438300_B24","doi-asserted-by":"crossref","first-page":"1870","DOI":"10.1093\/bioinformatics\/bth167","article-title":"Decomposition of metabolic network into functional modules based on the global connectivity structure of reaction graph","volume":"20","author":"Ma","year":"2004","journal-title":"Bioinformatics"},{"key":"2023013110163438300_B25","first-page":"536","article-title":"Linear-time modular decomposition and efficient transitive orientation of comparability graphs","volume-title":"SODA '94: Proceedings of the Fifth Annual ACM-SIAM Symposium on Discrete Algorithms. Society for Industrial and Applied Mathematics","author":"McConnell","year":"1994"},{"key":"2023013110163438300_B26","first-page":"257","article-title":"Substitution decomposition for discrete structures and connections with combinatorial optimization","volume":"19","author":"M\u00f6hring","year":"1984","journal-title":"Ann. Discrete Math."},{"key":"2023013110163438300_B27","doi-asserted-by":"crossref","first-page":"218","DOI":"10.1006\/meth.2001.1183","article-title":"The tandem affinity purification (tap) method: a general procedure of protein complex purification","volume":"24","author":"Puig","year":"2001","journal-title":"Methods"},{"key":"2023013110163438300_B28","doi-asserted-by":"crossref","first-page":"12123","DOI":"10.1073\/pnas.2032324100","article-title":"Protein complexes and functional modules in molecular networks","volume":"100","author":"Spirin","year":"2003","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023013110163438300_B29","doi-asserted-by":"crossref","first-page":"41","DOI":"10.7551\/mitpress\/9780262195485.003.0003","volume-title":"System Modeling in Cellular Biology: from Concepts to Nuts and Bolts. Modules and Modularity.","author":"Szallasi","year":"2006"},{"key":"2023013110163438300_B30","doi-asserted-by":"crossref","first-page":"3175","DOI":"10.1093\/emboj\/cdg296","article-title":"The nuclear actin-related proteins Arp7 and Arp9: a dimeric module that cooperates with architectural proteins for chromatin remodeling","volume":"22","author":"Szerlong","year":"2003","journal-title":"EMBO J."},{"key":"2023013110163438300_B31","doi-asserted-by":"crossref","first-page":"292","DOI":"10.1074\/mcp.M300005-MCP200","article-title":"Physical and functional modularity of the protein network in yeast","volume":"2","author":"Wilhelm","year":"2003","journal-title":"Mol. Cell Proteomics"},{"key":"2023013110163438300_B32","doi-asserted-by":"crossref","first-page":"e1000140","DOI":"10.1371\/journal.pcbi.1000140","article-title":"Why do hubs in the yeast protein interaction network tend to be essential: reexamining the connection between the network topology and essentiality","volume":"4","author":"Zotenko","year":"2008","journal-title":"PLoS Comput. Biol."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/25\/7\/926\/48983294\/bioinformatics_25_7_926.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/25\/7\/926\/48983294\/bioinformatics_25_7_926.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,31]],"date-time":"2023-01-31T20:20:33Z","timestamp":1675196433000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/25\/7\/926\/210962"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2009,2,17]]},"references-count":32,"journal-issue":{"issue":"7","published-print":{"date-parts":[[2009,4,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btp083","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2009,4,1]]},"published":{"date-parts":[[2009,2,17]]}}}