Preferential duplication in the sparse part of yeast protein interaction network

Gene duplication is an important mechanism driving the evolution of biomolecular network. Thus, it is expected that there should be a strong relationship between a gene's duplicability and the interactions of its protein product with other proteins in the network. We studied this question in th...

Ausführliche Beschreibung

Gespeichert in:
Bibliographische Detailangaben
Veröffentlicht in:Molecular biology and evolution 2006-12, Vol.23 (12), p.2467-2473
Hauptverfasser: Li, Li, Huang, Yingwu, Xia, Xuefeng, Sun, Zhirong
Format: Artikel
Sprache:eng
Schlagworte:
Online-Zugang:Volltext
Tags: Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!
container_end_page 2473
container_issue 12
container_start_page 2467
container_title Molecular biology and evolution
container_volume 23
creator Li, Li
Huang, Yingwu
Xia, Xuefeng
Sun, Zhirong
description Gene duplication is an important mechanism driving the evolution of biomolecular network. Thus, it is expected that there should be a strong relationship between a gene's duplicability and the interactions of its protein product with other proteins in the network. We studied this question in the context of the protein interaction network (PIN) of Saccharomyces cerevisiae. We found that duplicates have, on average, significantly lower clustering coefficient (CC) than singletons, and the proportion of duplicates (PD) decreases steadily with CC. Furthermore, using functional annotation data, we observed a strong negative correlation between PD and the mean CC for functional categories. By partitioning the network into modules and assigning each protein a modularity measure Q(n), we found that CC of a protein is a reflection of its modularity. Moreover, the core components of complexes identified in a recent high-throughput experiment, characterized by high CC, have lower PD than that of the attachments. Subsequently, 2 types of hub were identified by their degree, CC and Q(n). Although PD of intramodular hubs is much less than the network average, PD of intermodular hubs is comparable to, or even higher than, the network average. Our results suggest that high CC, and thus high modularity, pose strong evolutionary constraints on gene duplicability, and gene duplication prefers to happen in the sparse part of PINs.
doi_str_mv 10.1093/molbev/msl121
format Article
fullrecord <record><control><sourceid>proquest_cross</sourceid><recordid>TN_cdi_proquest_miscellaneous_68115101</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><sourcerecordid>19466336</sourcerecordid><originalsourceid>FETCH-LOGICAL-c361t-6fcdfd8da92794d919fb7e9aef0557b3e539aa49252459a0593401eb8262b57c3</originalsourceid><addsrcrecordid>eNqF0D1PwzAQgGELgWgpjKzIE1uoL47teEQVX1IlOsAcOclFBJI42A6o_56URGJk8Xl4dDq9hFwCuwGm-bq1TY5f69Y3EMMRWYLgKgIF-pgsmRr_CePpgpx5_84YJImUp2QBUqdMKLkku53DCh12oTYNLYe-qQsTatvRuqPhDanvjfNIxzdQW9E9Gh9o72zA-mACOlP8-g7Dt3Uf5-SkMo3Hi3muyOv93cvmMdo-PzxtbrdRwSWESFZFWZVpaXSsdFJq0FWuUBusmBAq5yi4NibRsYgToQ0TmicMME9jGedCFXxFrqe94y2fA_qQtbUvsGlMh3bwmUwBBDD4F4Iem3AuRxhNsHDW-zFL1ru6NW6fAcsOrbOpdTa1Hv3VvHjIWyz_9ByX_wBe6X1v</addsrcrecordid><sourcetype>Aggregation Database</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>19466336</pqid></control><display><type>article</type><title>Preferential duplication in the sparse part of yeast protein interaction network</title><source>MEDLINE</source><source>Access via Oxford University Press (Open Access Collection)</source><source>EZB-FREE-00999 freely available EZB journals</source><source>Alma/SFX Local Collection</source><source>Free Full-Text Journals in Chemistry</source><creator>Li, Li ; Huang, Yingwu ; Xia, Xuefeng ; Sun, Zhirong</creator><creatorcontrib>Li, Li ; Huang, Yingwu ; Xia, Xuefeng ; Sun, Zhirong</creatorcontrib><description>Gene duplication is an important mechanism driving the evolution of biomolecular network. Thus, it is expected that there should be a strong relationship between a gene's duplicability and the interactions of its protein product with other proteins in the network. We studied this question in the context of the protein interaction network (PIN) of Saccharomyces cerevisiae. We found that duplicates have, on average, significantly lower clustering coefficient (CC) than singletons, and the proportion of duplicates (PD) decreases steadily with CC. Furthermore, using functional annotation data, we observed a strong negative correlation between PD and the mean CC for functional categories. By partitioning the network into modules and assigning each protein a modularity measure Q(n), we found that CC of a protein is a reflection of its modularity. Moreover, the core components of complexes identified in a recent high-throughput experiment, characterized by high CC, have lower PD than that of the attachments. Subsequently, 2 types of hub were identified by their degree, CC and Q(n). Although PD of intramodular hubs is much less than the network average, PD of intermodular hubs is comparable to, or even higher than, the network average. Our results suggest that high CC, and thus high modularity, pose strong evolutionary constraints on gene duplicability, and gene duplication prefers to happen in the sparse part of PINs.</description><identifier>ISSN: 0737-4038</identifier><identifier>EISSN: 1537-1719</identifier><identifier>DOI: 10.1093/molbev/msl121</identifier><identifier>PMID: 16980576</identifier><language>eng</language><publisher>United States</publisher><subject>Cluster Analysis ; Fungal Proteins - genetics ; Fungal Proteins - metabolism ; Gene Duplication ; Genes, Fungal ; Protein Binding ; Protein Interaction Mapping ; Saccharomyces cerevisiae ; Saccharomyces cerevisiae - genetics ; Saccharomyces cerevisiae Proteins - genetics ; Saccharomyces cerevisiae Proteins - metabolism</subject><ispartof>Molecular biology and evolution, 2006-12, Vol.23 (12), p.2467-2473</ispartof><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c361t-6fcdfd8da92794d919fb7e9aef0557b3e539aa49252459a0593401eb8262b57c3</citedby></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>314,780,784,27924,27925</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/16980576$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Li, Li</creatorcontrib><creatorcontrib>Huang, Yingwu</creatorcontrib><creatorcontrib>Xia, Xuefeng</creatorcontrib><creatorcontrib>Sun, Zhirong</creatorcontrib><title>Preferential duplication in the sparse part of yeast protein interaction network</title><title>Molecular biology and evolution</title><addtitle>Mol Biol Evol</addtitle><description>Gene duplication is an important mechanism driving the evolution of biomolecular network. Thus, it is expected that there should be a strong relationship between a gene's duplicability and the interactions of its protein product with other proteins in the network. We studied this question in the context of the protein interaction network (PIN) of Saccharomyces cerevisiae. We found that duplicates have, on average, significantly lower clustering coefficient (CC) than singletons, and the proportion of duplicates (PD) decreases steadily with CC. Furthermore, using functional annotation data, we observed a strong negative correlation between PD and the mean CC for functional categories. By partitioning the network into modules and assigning each protein a modularity measure Q(n), we found that CC of a protein is a reflection of its modularity. Moreover, the core components of complexes identified in a recent high-throughput experiment, characterized by high CC, have lower PD than that of the attachments. Subsequently, 2 types of hub were identified by their degree, CC and Q(n). Although PD of intramodular hubs is much less than the network average, PD of intermodular hubs is comparable to, or even higher than, the network average. Our results suggest that high CC, and thus high modularity, pose strong evolutionary constraints on gene duplicability, and gene duplication prefers to happen in the sparse part of PINs.</description><subject>Cluster Analysis</subject><subject>Fungal Proteins - genetics</subject><subject>Fungal Proteins - metabolism</subject><subject>Gene Duplication</subject><subject>Genes, Fungal</subject><subject>Protein Binding</subject><subject>Protein Interaction Mapping</subject><subject>Saccharomyces cerevisiae</subject><subject>Saccharomyces cerevisiae - genetics</subject><subject>Saccharomyces cerevisiae Proteins - genetics</subject><subject>Saccharomyces cerevisiae Proteins - metabolism</subject><issn>0737-4038</issn><issn>1537-1719</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2006</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqF0D1PwzAQgGELgWgpjKzIE1uoL47teEQVX1IlOsAcOclFBJI42A6o_56URGJk8Xl4dDq9hFwCuwGm-bq1TY5f69Y3EMMRWYLgKgIF-pgsmRr_CePpgpx5_84YJImUp2QBUqdMKLkku53DCh12oTYNLYe-qQsTatvRuqPhDanvjfNIxzdQW9E9Gh9o72zA-mACOlP8-g7Dt3Uf5-SkMo3Hi3muyOv93cvmMdo-PzxtbrdRwSWESFZFWZVpaXSsdFJq0FWuUBusmBAq5yi4NibRsYgToQ0TmicMME9jGedCFXxFrqe94y2fA_qQtbUvsGlMh3bwmUwBBDD4F4Iem3AuRxhNsHDW-zFL1ru6NW6fAcsOrbOpdTa1Hv3VvHjIWyz_9ByX_wBe6X1v</recordid><startdate>20061201</startdate><enddate>20061201</enddate><creator>Li, Li</creator><creator>Huang, Yingwu</creator><creator>Xia, Xuefeng</creator><creator>Sun, Zhirong</creator><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>8FD</scope><scope>FR3</scope><scope>M7N</scope><scope>P64</scope><scope>RC3</scope><scope>7X8</scope></search><sort><creationdate>20061201</creationdate><title>Preferential duplication in the sparse part of yeast protein interaction network</title><author>Li, Li ; Huang, Yingwu ; Xia, Xuefeng ; Sun, Zhirong</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c361t-6fcdfd8da92794d919fb7e9aef0557b3e539aa49252459a0593401eb8262b57c3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2006</creationdate><topic>Cluster Analysis</topic><topic>Fungal Proteins - genetics</topic><topic>Fungal Proteins - metabolism</topic><topic>Gene Duplication</topic><topic>Genes, Fungal</topic><topic>Protein Binding</topic><topic>Protein Interaction Mapping</topic><topic>Saccharomyces cerevisiae</topic><topic>Saccharomyces cerevisiae - genetics</topic><topic>Saccharomyces cerevisiae Proteins - genetics</topic><topic>Saccharomyces cerevisiae Proteins - metabolism</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Li, Li</creatorcontrib><creatorcontrib>Huang, Yingwu</creatorcontrib><creatorcontrib>Xia, Xuefeng</creatorcontrib><creatorcontrib>Sun, Zhirong</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Technology Research Database</collection><collection>Engineering Research Database</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><jtitle>Molecular biology and evolution</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Li, Li</au><au>Huang, Yingwu</au><au>Xia, Xuefeng</au><au>Sun, Zhirong</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Preferential duplication in the sparse part of yeast protein interaction network</atitle><jtitle>Molecular biology and evolution</jtitle><addtitle>Mol Biol Evol</addtitle><date>2006-12-01</date><risdate>2006</risdate><volume>23</volume><issue>12</issue><spage>2467</spage><epage>2473</epage><pages>2467-2473</pages><issn>0737-4038</issn><eissn>1537-1719</eissn><abstract>Gene duplication is an important mechanism driving the evolution of biomolecular network. Thus, it is expected that there should be a strong relationship between a gene's duplicability and the interactions of its protein product with other proteins in the network. We studied this question in the context of the protein interaction network (PIN) of Saccharomyces cerevisiae. We found that duplicates have, on average, significantly lower clustering coefficient (CC) than singletons, and the proportion of duplicates (PD) decreases steadily with CC. Furthermore, using functional annotation data, we observed a strong negative correlation between PD and the mean CC for functional categories. By partitioning the network into modules and assigning each protein a modularity measure Q(n), we found that CC of a protein is a reflection of its modularity. Moreover, the core components of complexes identified in a recent high-throughput experiment, characterized by high CC, have lower PD than that of the attachments. Subsequently, 2 types of hub were identified by their degree, CC and Q(n). Although PD of intramodular hubs is much less than the network average, PD of intermodular hubs is comparable to, or even higher than, the network average. Our results suggest that high CC, and thus high modularity, pose strong evolutionary constraints on gene duplicability, and gene duplication prefers to happen in the sparse part of PINs.</abstract><cop>United States</cop><pmid>16980576</pmid><doi>10.1093/molbev/msl121</doi><tpages>7</tpages><oa>free_for_read</oa></addata></record>
fulltext fulltext
identifier ISSN: 0737-4038
ispartof Molecular biology and evolution, 2006-12, Vol.23 (12), p.2467-2473
issn 0737-4038
1537-1719
language eng
recordid cdi_proquest_miscellaneous_68115101
source MEDLINE; Access via Oxford University Press (Open Access Collection); EZB-FREE-00999 freely available EZB journals; Alma/SFX Local Collection; Free Full-Text Journals in Chemistry
subjects Cluster Analysis
Fungal Proteins - genetics
Fungal Proteins - metabolism
Gene Duplication
Genes, Fungal
Protein Binding
Protein Interaction Mapping
Saccharomyces cerevisiae
Saccharomyces cerevisiae - genetics
Saccharomyces cerevisiae Proteins - genetics
Saccharomyces cerevisiae Proteins - metabolism
title Preferential duplication in the sparse part of yeast protein interaction network
url https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2024-12-23T05%3A59%3A40IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-proquest_cross&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Preferential%20duplication%20in%20the%20sparse%20part%20of%20yeast%20protein%20interaction%20network&rft.jtitle=Molecular%20biology%20and%20evolution&rft.au=Li,%20Li&rft.date=2006-12-01&rft.volume=23&rft.issue=12&rft.spage=2467&rft.epage=2473&rft.pages=2467-2473&rft.issn=0737-4038&rft.eissn=1537-1719&rft_id=info:doi/10.1093/molbev/msl121&rft_dat=%3Cproquest_cross%3E19466336%3C/proquest_cross%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=19466336&rft_id=info:pmid/16980576&rfr_iscdi=true