From Corynebacterium glutamicum to Mycobacterium tuberculosis--towards transfers of gene regulatory networks and integrated data analyses with MycoRegNet.
From Corynebacterium glutamicum to Mycobacterium tuberculosis--towards transfers of gene regulatory networks and integrated data analyses with MycoRegNet.
复制标题
DOI：
10.1093/nar/gkp453
复制
发表时间：
2009-08
影响因子：
14.9
通讯作者：
Baumbach J
中科院分区：
文献类型：
--
作者：
Krawczyk J;Kohl TA;Goesmann A;Kalinowski J;Baumbach J
每年，大约有200万人死于结核病，这是一种由结核分枝杆菌引起的疾病。人们迫切需要新的抗结核疗法（抗结核药）和药物来科普结核病的传播。尽管许多努力，以获得更好地了解M。结核病的致病性及其在人类中的生存策略，许多问题仍然没有得到解决。在细菌的其他细胞过程中，致病性是由转录调控控制的。因此，对M.结核分枝杆菌的研究集中在转录调控的分析上，以获得关于致病性和确保分枝杆菌存活的其他基本过程的新见解。我们设计了一个生物信息学管道，用于在分类学上密切相关的生物体之间可靠地转移基因调控，该管道包括（i）预测直链基因和（ii）预测转录因子结合位点。总共确定了M的460种调节相互作用。肺结核使用我们的比较方法。在此基础上，我们设计了一个公共平台MycoRegNet，旨在对分枝杆菌转录基因调控网络进行数据整合、分析、可视化和最终重建。它是一个全面的数据库系统和分析平台，提供了多种数据探索和新假设生成的方法。MycoRegNet可在http://mycoregnet.cebitec.uni-bielefeld.de上公开获取。
Year by year, approximately two million people die from tuberculosis, a disease caused by the bacterium Mycobacterium tuberculosis. There is a tremendous need for new anti-tuberculosis therapies (antituberculotica) and drugs to cope with the spread of tuberculosis. Despite many efforts to obtain a better understanding of M. tuberculosis' pathogenicity and its survival strategy in humans, many questions are still unresolved. Among other cellular processes in bacteria, pathogenicity is controlled by transcriptional regulation. Thus, various studies on M. tuberculosis concentrate on the analysis of transcriptional regulation in order to gain new insights on pathogenicity and other essential processes ensuring mycobacterial survival. We designed a bioinformatics pipeline for the reliable transfer of gene regulations between taxonomically closely related organisms that incorporates (i) a prediction of orthologous genes and (ii) the prediction of transcription factor binding sites. In total, 460 regulatory interactions were identified for M. tuberculosis using our comparative approach. Based on that, we designed a publicly available platform that aims to data integration, analysis, visualization and finally the reconstruction of mycobacterial transcriptional gene regulatory networks: MycoRegNet. It is a comprehensive database system and analysis platform that offers several methods for data exploration and the generation of novel hypotheses. MycoRegNet is publicly available at http://mycoregnet.cebitec.uni-bielefeld.de.
登录
查看更多内容
影响因子：
3
作者：
Dondrup, Michael;Albaum, Stefan P.;Griebel, Thasso;Henckel, Kolja;Juenemann, Sebastian;Kahlke, Tim;Kleindt, Christiane K.;Kuester, Helge;Linke, Burkhard;Mertens, Dominik;Mittard-Runte, Virginie;Neuweger, Heiko;Runte, Kai J.;Tauch, Andreas;Tille, Felix;Puehler, Alfred;Goesmann, Alexander
通讯作者：
Goesmann, Alexander
影响因子：
14.9
作者：
Benson DA;Cavanaugh M;Clark K;Karsch-Mizrachi I;Lipman DJ;Ostell J;Sayers EW
通讯作者：
Sayers EW
影响因子：
2.8
作者：
Agarwal, Nisheeth;Raghunand, Tirumalai R.;Bishai, William R.
通讯作者：
Bishai, William R.
影响因子：
5.6
作者：
Babu, MM;Teichmann, SA;Aravind, L
通讯作者：
Aravind, L
影响因子：
2.8
作者：
Han, Sung Ok;Inui, Masayuki;Yukawa, Hideaki
通讯作者：
Yukawa, Hideaki