CoryneRegNet 4.0 - A reference database for corynebacterial gene regulatory networks.
CoryneRegNet 4.0 - A reference database for corynebacterial gene regulatory networks.
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DOI：
10.1186/1471-2105-8-429
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发表时间：
2007-11-06
影响因子：
3
通讯作者：
Baumbach J
中科院分区：
文献类型：
--
作者：
Baumbach J
从文献知识、计算机预测和全球DNA微阵列杂交实验中推导出的DNA结合转录因子(基因表达调控的关键角色)和微生物转录调控相互作用的详细信息，为转录调控网络的全基因组分析开辟了道路。这些网络的大规模重建使得能够对细胞行为进行计算机分析，以响应不断变化的环境条件。我们之前发布了CoryneRegNet，这是一个基于本体的棒状杆菌转录因子和调控网络的数据仓库。最初，它的设计是为了提供谷氨酸棒杆菌基因调控网络的分析和可视化方法。现在我们介绍CoryneRegNet Release 4.0，它集成了4个棒状细菌、2个分枝杆菌和模式生物大肠杆菌K12的基因调控网络数据。与之前的版本一样，CoryneRegNet提供了一个基于Web的用户界面，以访问数据库内容，允许进行各种查询，并支持在不同层级重建、分析和可视化监管网络。在本文中，我们介绍了CoryneRegNet的进一步改进的数据库内容以及新的分析功能。网络可视化功能GraphVis现在允许对重建的基因调控网络进行物种间比较，并将基因表达水平投影到该网络上。因此，我们将Stimulon数据直接添加到数据库中，还提供了Web Service访问DNA微阵列分析平台EMMA。此外，CoryneRegNet现在提供了一个基于SOAP的Web服务服务器，该服务器可以很容易地被其他生物信息学软件系统使用。刺激物(从数据库导入，或由用户上传)可以在已知转录调控网络的背景下进行分析，以预测假定的矛盾或进一步的基因调控相互作用。此外，它通过启发式地解决加权图簇编辑问题来整合蛋白质簇。此外，它还提供对来自GenDB的最新基因注释数据的基于Web服务的访问。CoryneRegNet 4.0版是一个集成分析原核基因调控网络的综合系统。它是一个通用的系统生物学平台，支持对微生物中基因表达转录调控的高效和大规模分析。该报告可在以下网址公开获取。
Detailed information on DNA-binding transcription factors (the key players in the regulation of gene expression) and on transcriptional regulatory interactions of microorganisms deduced from literature-derived knowledge, computer predictions and global DNA microarray hybridization experiments, has opened the way for the genome-wide analysis of transcriptional regulatory networks. The large-scale reconstruction of these networks allows the in silico analysis of cell behavior in response to changing environmental conditions. We previously published CoryneRegNet, an ontology-based data warehouse of corynebacterial transcription factors and regulatory networks. Initially, it was designed to provide methods for the analysis and visualization of the gene regulatory network of Corynebacterium glutamicum. Now we introduce CoryneRegNet release 4.0, which integrates data on the gene regulatory networks of 4 corynebacteria, 2 mycobacteria and the model organism Escherichia coli K12. As the previous versions, CoryneRegNet provides a web-based user interface to access the database content, to allow various queries, and to support the reconstruction, analysis and visualization of regulatory networks at different hierarchical levels. In this article, we present the further improved database content of CoryneRegNet along with novel analysis features. The network visualization feature GraphVis now allows the inter-species comparisons of reconstructed gene regulatory networks and the projection of gene expression levels onto that networks. Therefore, we added stimulon data directly into the database, but also provide Web Service access to the DNA microarray analysis platform EMMA. Additionally, CoryneRegNet now provides a SOAP based Web Service server, which can easily be consumed by other bioinformatics software systems. Stimulons (imported from the database, or uploaded by the user) can be analyzed in the context of known transcriptional regulatory networks to predict putative contradictions or further gene regulatory interactions. Furthermore, it integrates protein clusters by means of heuristically solving the weighted graph cluster editing problem. In addition, it provides Web Service based access to up to date gene annotation data from GenDB. The release 4.0 of CoryneRegNet is a comprehensive system for the integrated analysis of procaryotic gene regulatory networks. It is a versatile systems biology platform to support the efficient and large-scale analysis of transcriptional regulation of gene expression in microorganisms. It is publicly available at .
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影响因子：
4.1
作者：
Dondrup, M;Goesmann, A;Meyer, F
通讯作者：
Meyer, F
影响因子：
4.1
作者：
Hüser, AT;Becker, A;Tauch, A
通讯作者：
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影响因子：
5.6
作者：
Babu, MM;Teichmann, SA;Aravind, L
通讯作者：
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影响因子：
4.4
作者：
Larisch, Christof;Nakunst, Diana;Huser, Andrea T;Tauch, Andreas;Kalinowski, Jorn
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Kalinowski, Jorn
基于快速索引的算法和用于匹配位置特定评分矩阵的软件。
影响因子：
3
作者：
Beckstette M;Homann R;Giegerich R;Kurtz S
通讯作者：
Kurtz S