Identifying the Modular Structures in Protein Interaction Networks
Identifying the modular structures in Protein Interaction Networks (PINs) is crucial to the understanding of the organization and function of biological systems. We propose a new module definition taking into account the degree of a subgraph instead of a vertice, and design a corresponding agglomera...
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| creator | Li, Yanen Lu, Feng Zhou, Yanhong |
| description | Identifying the modular structures in Protein Interaction Networks (PINs) is crucial to the understanding of the organization and function of biological systems. We propose a new module definition taking into account the degree of a subgraph instead of a vertice, and design a corresponding agglomerative algorithm, which is implemented into a computational tool called ModuleSpider, to recognize modules within a network. The application of ModuleSpider to the yeast core protein interaction network identifies 97 simple modules which are biologically meaningful according to the GO annotation of proteins in the modules. In addition, the results of comparison analysis demonstrate that ModuleSpider modules show stronger biological relevance. Further, the ModuleSpider is able to construct the interaction web of modules, which provides insights to the high level relationships of different functional modules. ModuleSpider is freely available upon request to the authors. |
| doi_str_mv | 10.1007/11816102_80 |
| format | Book Chapter |
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We propose a new module definition taking into account the degree of a subgraph instead of a vertice, and design a corresponding agglomerative algorithm, which is implemented into a computational tool called ModuleSpider, to recognize modules within a network. The application of ModuleSpider to the yeast core protein interaction network identifies 97 simple modules which are biologically meaningful according to the GO annotation of proteins in the modules. In addition, the results of comparison analysis demonstrate that ModuleSpider modules show stronger biological relevance. Further, the ModuleSpider is able to construct the interaction web of modules, which provides insights to the high level relationships of different functional modules. ModuleSpider is freely available upon request to the authors.</description><identifier>ISSN: 0302-9743</identifier><identifier>ISBN: 9783540372776</identifier><identifier>ISBN: 3540372776</identifier><identifier>EISSN: 1611-3349</identifier><identifier>EISBN: 9783540372820</identifier><identifier>EISBN: 3540372822</identifier><identifier>DOI: 10.1007/11816102_80</identifier><language>eng</language><publisher>Berlin, Heidelberg: Springer Berlin Heidelberg</publisher><subject>Modular Structure ; Protein Interaction Network ; Simple Module ; Strong Module ; Weak Module</subject><ispartof>Computational Intelligence and Bioinformatics, 2006, p.757-767</ispartof><rights>Springer-Verlag Berlin Heidelberg 2006</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><relation>Lecture Notes in Computer Science</relation></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://link.springer.com/content/pdf/10.1007/11816102_80$$EPDF$$P50$$Gspringer$$H</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1007/11816102_80$$EHTML$$P50$$Gspringer$$H</linktohtml><link.rule.ids>779,780,784,793,27924,38254,41441,42510</link.rule.ids></links><search><contributor>Li, Kang</contributor><contributor>Huang, De-Shuang</contributor><contributor>Irwin, George William</contributor><creatorcontrib>Li, Yanen</creatorcontrib><creatorcontrib>Lu, Feng</creatorcontrib><creatorcontrib>Zhou, Yanhong</creatorcontrib><title>Identifying the Modular Structures in Protein Interaction Networks</title><title>Computational Intelligence and Bioinformatics</title><description>Identifying the modular structures in Protein Interaction Networks (PINs) is crucial to the understanding of the organization and function of biological systems. We propose a new module definition taking into account the degree of a subgraph instead of a vertice, and design a corresponding agglomerative algorithm, which is implemented into a computational tool called ModuleSpider, to recognize modules within a network. The application of ModuleSpider to the yeast core protein interaction network identifies 97 simple modules which are biologically meaningful according to the GO annotation of proteins in the modules. In addition, the results of comparison analysis demonstrate that ModuleSpider modules show stronger biological relevance. Further, the ModuleSpider is able to construct the interaction web of modules, which provides insights to the high level relationships of different functional modules. ModuleSpider is freely available upon request to the authors.</description><subject>Modular Structure</subject><subject>Protein Interaction Network</subject><subject>Simple Module</subject><subject>Strong Module</subject><subject>Weak Module</subject><issn>0302-9743</issn><issn>1611-3349</issn><isbn>9783540372776</isbn><isbn>3540372776</isbn><isbn>9783540372820</isbn><isbn>3540372822</isbn><fulltext>true</fulltext><rsrctype>book_chapter</rsrctype><creationdate>2006</creationdate><recordtype>book_chapter</recordtype><sourceid/><recordid>eNpNUEtLxDAYjC-wrD35B3r1UP2SL2mSoy6uFtYHqOeStonWXVpJUsR_bxY97FyGYWCYGULOKVxSAHlFqaIVBdYoOCC5lgoFB5RMMTgkWbJoicj10b4nZXVMMkBgpZYcT0kewickIK2kgozc1L0d4-B-hvG9iB-2eJj6eWt88RL93MXZ21AMY_Hsp2gT12O03nRxmMbi0cbvyW_CGTlxZhts_s8L8ra6fV3el-unu3p5vS4DVTqWbe-40KJF1WkLTlmRpJG9bY1hVGPP29RKOq64YMi6ToBl0O4mcJAOcUEu_nLDl09trW_aadqEhkKz-6fZ-wd_AYn8Ufc</recordid><startdate>2006</startdate><enddate>2006</enddate><creator>Li, Yanen</creator><creator>Lu, Feng</creator><creator>Zhou, Yanhong</creator><general>Springer Berlin Heidelberg</general><scope/></search><sort><creationdate>2006</creationdate><title>Identifying the Modular Structures in Protein Interaction Networks</title><author>Li, Yanen ; Lu, Feng ; Zhou, Yanhong</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-s189t-bdf4595b38c9e0f8e5459a7debaa2193d4b0317f4845232cc50e20b2776407f33</frbrgroupid><rsrctype>book_chapters</rsrctype><prefilter>book_chapters</prefilter><language>eng</language><creationdate>2006</creationdate><topic>Modular Structure</topic><topic>Protein Interaction Network</topic><topic>Simple Module</topic><topic>Strong Module</topic><topic>Weak Module</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Li, Yanen</creatorcontrib><creatorcontrib>Lu, Feng</creatorcontrib><creatorcontrib>Zhou, Yanhong</creatorcontrib></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Li, Yanen</au><au>Lu, Feng</au><au>Zhou, Yanhong</au><au>Li, Kang</au><au>Huang, De-Shuang</au><au>Irwin, George William</au><format>book</format><genre>bookitem</genre><ristype>CHAP</ristype><atitle>Identifying the Modular Structures in Protein Interaction Networks</atitle><btitle>Computational Intelligence and Bioinformatics</btitle><seriestitle>Lecture Notes in Computer Science</seriestitle><date>2006</date><risdate>2006</risdate><spage>757</spage><epage>767</epage><pages>757-767</pages><issn>0302-9743</issn><eissn>1611-3349</eissn><isbn>9783540372776</isbn><isbn>3540372776</isbn><eisbn>9783540372820</eisbn><eisbn>3540372822</eisbn><abstract>Identifying the modular structures in Protein Interaction Networks (PINs) is crucial to the understanding of the organization and function of biological systems. We propose a new module definition taking into account the degree of a subgraph instead of a vertice, and design a corresponding agglomerative algorithm, which is implemented into a computational tool called ModuleSpider, to recognize modules within a network. The application of ModuleSpider to the yeast core protein interaction network identifies 97 simple modules which are biologically meaningful according to the GO annotation of proteins in the modules. In addition, the results of comparison analysis demonstrate that ModuleSpider modules show stronger biological relevance. Further, the ModuleSpider is able to construct the interaction web of modules, which provides insights to the high level relationships of different functional modules. ModuleSpider is freely available upon request to the authors.</abstract><cop>Berlin, Heidelberg</cop><pub>Springer Berlin Heidelberg</pub><doi>10.1007/11816102_80</doi><tpages>11</tpages></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 0302-9743 |
| ispartof | Computational Intelligence and Bioinformatics, 2006, p.757-767 |
| issn | 0302-9743 1611-3349 |
| language | eng |
| recordid | cdi_springer_books_10_1007_11816102_80 |
| source | Springer Books |
| subjects | Modular Structure Protein Interaction Network Simple Module Strong Module Weak Module |
| title | Identifying the Modular Structures in Protein Interaction Networks |
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