@ARTICLE{TreeBASE2Ref23553,
author = {maxime huvet and Michael P.H Stumpf},
title = {Overlapping genes: a window on gene evolvability.},
year = {2014},
keywords = {Overlapping genes, evolution, expression regulation, operon},
doi = {},
url = {http://},
pmid = {},
journal = {BMC genomics},
volume = {},
number = {},
pages = {},
abstract = {Background
The forces underlying genome architecture and organization are still only poorly
understood in detail. Overlapping genes (genes partially or entirely overlapping) represent
a genomic feature that is shared widely between biological organisms ranging from viruses
to multi-cellular organisms. In bacteria, a third of the annotated genes are involved in an
overlap. Despite the widespread nature of this arrangement, its evolutionary origins and
biological ramifications have so far eluded explanation.
Results
Here we present a comparative approach using information from 699 bacterial genomes
that sheds light on the evolutionary dynamics of overlapping genes. We show that these
structures exhibit high levels of plasticity.
Conclusions
We propose a simple model allowing us to explain the observed properties of overlapping
genes based on the importance of initiation and termination of transcriptional and
translational processes. We believe that taking into account the processes leading to the
expression of protein-coding genes hold the key to the understanding of overlapping
genes structures.}
}
Citation for Study 16248
Citation tit
Yikes!
javax.el.ELException: Error reading [person] on type [org.cipres.treebase.domain.admin.User$$EnhancerByCGLIB$$bd1018be] at javax.el.BeanELResolver.getValue(BeanELResolver.java:104) at org.apache.jasper.el.JasperELResolver.getValue(JasperELResolver.java:112) at org.apache.el.parser.AstValue.getValue(AstValue.java:168) at org.apache.el.parser.AstEqual.getValue(AstEqual.java:37) at org.apache.el.ValueExpressionImpl.getValue(ValueExpressionImpl.java:189) at org.apache.jasper.runtime.PageContextImpl.proprietaryEvaluate(PageContextImpl.java:942) at org.apache.jsp.WEB_002dINF.pages.search.study.summary_jsp._jspx_meth_c_005fif_005f2(summary_jsp.java:661) at org.apache.jsp.WEB_002dINF.pages.search.study.summary_jsp._jspx_meth_c_005fforEach_005f0(summary_jsp.java:590) at org.apache.jsp.WEB_002dINF.pages.search.study.summary_jsp._jspx_meth_c_005fif_005f1(summary_jsp.java:541) at org.apache.jsp.WEB_002dINF.pages.search.study.summary_jsp._jspx_meth_c_005fif_005f0(summary_jsp.java:479) at org.apache.jsp.WEB_002dINF.pages.search.study.summary_jsp._jspService(summary_jsp.java:188) at org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:70) at javax.servlet.http.HttpServlet.service(HttpServlet.java:583) at org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:465) at org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:383) at org.apache.jasper.servlet.JspServlet.service(JspServlet.java:331) at javax.servlet.http.HttpServlet.service(HttpServlet.java:583) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:212) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:156) at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:51) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:181) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:156) at com.opensymphony.module.sitemesh.filter.PageFilter.doFilter(PageFilter.java:39) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:181) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:156) at org.apache.catalina.core.ApplicationDispatcher.invoke(ApplicationDispatcher.java:662) at org.apache.catalina.core.ApplicationDispatcher.processRequest(ApplicationDispatcher.java:428) at org.apache.catalina.core.ApplicationDispatcher.doForward(ApplicationDispatcher.java:360) at org.apache.catalina.core.ApplicationDispatcher.forward(ApplicationDispatcher.java:297) at sun.reflect.GeneratedMethodAccessor287.invoke(Unknown Source) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:498) at net.bull.javamelody.JspWrapper.invoke(JspWrapper.java:152) at net.bull.javamelody.JdbcWrapper$DelegatingInvocationHandler.invoke(JdbcWrapper.java:294) at com.sun.proxy.$Proxy159.forward(Unknown Source) at org.springframework.web.servlet.view.InternalResourceView.renderMergedOutputModel(InternalResourceView.java:142) at org.springframework.web.servlet.view.AbstractView.render(AbstractView.java:239) at org.springframework.web.servlet.DispatcherServlet.render(DispatcherServlet.java:1142) at org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:879) at org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:792) at org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:476) at org.springframework.web.servlet.FrameworkServlet.doGet(FrameworkServlet.java:431) at javax.servlet.http.HttpServlet.service(HttpServlet.java:489) at javax.servlet.http.HttpServlet.service(HttpServlet.java:583) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:212) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:156) at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:51) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:181) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:156) at net.bull.javamelody.MonitoringFilter.doFilter(MonitoringFilter.java:239) at net.bull.javamelody.MonitoringFilter.doFilter(MonitoringFilter.java:215) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:181) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:156) at org.tuckey.web.filters.urlrewrite.RuleChain.handleRewrite(RuleChain.java:164) at org.tuckey.web.filters.urlrewrite.RuleChain.doRules(RuleChain.java:141) at org.tuckey.web.filters.urlrewrite.UrlRewriter.processRequest(UrlRewriter.java:90) at org.tuckey.web.filters.urlrewrite.UrlRewriteFilter.doFilter(UrlRewriteFilter.java:406) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:181) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:156) at org.displaytag.filter.ResponseOverrideFilter.doFilter(ResponseOverrideFilter.java:125) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:181) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:156) at org.springframework.orm.hibernate3.support.OpenSessionInViewFilter.doFilterInternal(OpenSessionInViewFilter.java:198) at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:75) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:181) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:156) at com.opensymphony.module.sitemesh.filter.PageFilter.parsePage(PageFilter.java:119) at com.opensymphony.module.sitemesh.filter.PageFilter.doFilter(PageFilter.java:55) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:181) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:156) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:264) at org.acegisecurity.intercept.web.FilterSecurityInterceptor.invoke(FilterSecurityInterceptor.java:107) at org.acegisecurity.intercept.web.FilterSecurityInterceptor.doFilter(FilterSecurityInterceptor.java:72) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.ui.ExceptionTranslationFilter.doFilter(ExceptionTranslationFilter.java:110) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.wrapper.SecurityContextHolderAwareRequestFilter.doFilter(SecurityContextHolderAwareRequestFilter.java:81) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.ui.AbstractProcessingFilter.doFilter(AbstractProcessingFilter.java:217) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.context.HttpSessionContextIntegrationFilter.doFilter(HttpSessionContextIntegrationFilter.java:191) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.util.FilterChainProxy.doFilter(FilterChainProxy.java:148) at org.acegisecurity.util.FilterToBeanProxy.doFilter(FilterToBeanProxy.java:90) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:181) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:156) at net.bull.javamelody.MonitoringFilter.doFilter(MonitoringFilter.java:199) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:181) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:156) at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:168) at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:90) at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:483) at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:130) at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:93) at org.apache.catalina.valves.AbstractAccessLogValve.invoke(AbstractAccessLogValve.java:679) at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:74) at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:342) at org.apache.coyote.http11.Http11Processor.service(Http11Processor.java:617) at org.apache.coyote.AbstractProcessorLight.process(AbstractProcessorLight.java:63) at org.apache.coyote.AbstractProtocol$ConnectionHandler.process(AbstractProtocol.java:934) at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1698) at org.apache.tomcat.util.net.SocketProcessorBase.run(SocketProcessorBase.java:52) at org.apache.tomcat.util.threads.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1191) at org.apache.tomcat.util.threads.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:659) at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61) at java.lang.Thread.run(Thread.java:750) Caused by: org.hibernate.exception.GenericJDBCException: could not load an entity: [org.cipres.treebase.domain.admin.User#13001] at org.hibernate.exception.SQLStateConverter.handledNonSpecificException(SQLStateConverter.java:103) at org.hibernate.exception.SQLStateConverter.convert(SQLStateConverter.java:91) at org.hibernate.exception.JDBCExceptionHelper.convert(JDBCExceptionHelper.java:43) at org.hibernate.loader.Loader.loadEntity(Loader.java:1874) at org.hibernate.loader.entity.AbstractEntityLoader.load(AbstractEntityLoader.java:48) at org.hibernate.loader.entity.AbstractEntityLoader.load(AbstractEntityLoader.java:42) at org.hibernate.loader.entity.BatchingEntityLoader.load(BatchingEntityLoader.java:82) at org.hibernate.persister.entity.AbstractEntityPersister.load(AbstractEntityPersister.java:3049) at org.hibernate.event.def.DefaultLoadEventListener.loadFromDatasource(DefaultLoadEventListener.java:399) at org.hibernate.event.def.DefaultLoadEventListener.doLoad(DefaultLoadEventListener.java:375) at org.hibernate.event.def.DefaultLoadEventListener.load(DefaultLoadEventListener.java:139) at org.hibernate.event.def.DefaultLoadEventListener.onLoad(DefaultLoadEventListener.java:98) at org.hibernate.impl.SessionImpl.fireLoad(SessionImpl.java:878) at org.hibernate.impl.SessionImpl.immediateLoad(SessionImpl.java:836) at org.hibernate.proxy.AbstractLazyInitializer.initialize(AbstractLazyInitializer.java:66) at org.hibernate.proxy.AbstractLazyInitializer.getImplementation(AbstractLazyInitializer.java:111) at org.hibernate.proxy.pojo.cglib.CGLIBLazyInitializer.invoke(CGLIBLazyInitializer.java:150) at org.cipres.treebase.domain.admin.User$$EnhancerByCGLIB$$bd1018be.getPerson() at sun.reflect.GeneratedMethodAccessor390.invoke(Unknown Source) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:498) at javax.el.BeanELResolver.getValue(BeanELResolver.java:99) ... 105 more Caused by: org.postgresql.util.PSQLException: This statement has been closed. at org.postgresql.jdbc.PgStatement.checkClosed(PgStatement.java:742) at org.postgresql.jdbc.PgStatement.getMaxRows(PgStatement.java:546) at org.postgresql.jdbc.PgStatement.createResultSet(PgStatement.java:171) at org.postgresql.jdbc.PgStatement$StatementResultHandler.handleResultRows(PgStatement.java:222) at org.postgresql.core.ResultHandlerDelegate.handleResultRows(ResultHandlerDelegate.java:31) at org.postgresql.core.v3.QueryExecutorImpl$1.handleResultRows(QueryExecutorImpl.java:612) at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:2307) at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:356) at org.postgresql.jdbc.PgStatement.executeInternal(PgStatement.java:496) at org.postgresql.jdbc.PgStatement.execute(PgStatement.java:413) at org.postgresql.jdbc.PgPreparedStatement.executeWithFlags(PgPreparedStatement.java:190) at org.postgresql.jdbc.PgPreparedStatement.executeQuery(PgPreparedStatement.java:134) at org.apache.tomcat.dbcp.dbcp2.DelegatingPreparedStatement.executeQuery(DelegatingPreparedStatement.java:106) at org.apache.tomcat.dbcp.dbcp2.DelegatingPreparedStatement.executeQuery(DelegatingPreparedStatement.java:106) at org.hibernate.jdbc.AbstractBatcher.getResultSet(AbstractBatcher.java:186) at org.hibernate.loader.Loader.getResultSet(Loader.java:1787) at org.hibernate.loader.Loader.doQuery(Loader.java:674) at org.hibernate.loader.Loader.doQueryAndInitializeNonLazyCollections(Loader.java:236) at org.hibernate.loader.Loader.loadEntity(Loader.java:1860) ... 123 more