Department of Plant Systems Biology, Flanders Institute for Biotechnology, Ghent University, 9052 Ghent, Belgium.
Plant Physiol. 2010 Mar;152(3):1167-79. doi: 10.1104/pp.109.147215. Epub 2010 Jan 6.
As an overwhelming amount of functional genomics data have been generated, the retrieval, integration, and interpretation of these data need to be facilitated to enable the advance of (systems) biological research. For example, gathering and processing microarray data that are related to a particular biological process is not straightforward, nor is the compilation of protein-protein interactions from numerous partially overlapping databases identified through diverse approaches. However, these tasks are inevitable to address the following questions. Does a group of differentially expressed genes show similar expression in diverse microarray experiments? Was an identified protein-protein interaction previously detected by other approaches? Are the interacting proteins encoded by genes with similar expression profiles and localization? We developed CORNET (for CORrelation NETworks) as an access point to transcriptome, protein interactome, and localization data and functional information on Arabidopsis (Arabidopsis thaliana). It consists of two flexible and versatile tools, namely the coexpression tool and the protein-protein interaction tool. The ability to browse and search microarray experiments using ontology terms and the incorporation of personal microarray data are distinctive features of the microarray repository. The coexpression tool enables either the alternate or simultaneous use of diverse expression compendia, whereas the protein-protein interaction tool searches experimentally and computationally identified protein-protein interactions. Different search options are implemented to enable the construction of coexpression and/or protein-protein interaction networks centered around multiple input genes or proteins. Moreover, networks and associated evidence are visualized in Cytoscape. Localization is visualized in pie charts, thereby allowing multiple localizations per protein. CORNET is available at http://bioinformatics.psb.ugent.be/cornet.
随着大量功能基因组学数据的产生，需要方便地检索、整合和解释这些数据，以推动（系统）生物学研究的进展。例如，收集和处理与特定生物过程相关的微阵列数据并不简单，也不容易从众多部分重叠的数据库中编译通过各种方法识别的蛋白质-蛋白质相互作用。然而，这些任务是不可避免的，需要解决以下问题。一组差异表达的基因在不同的微阵列实验中是否表现出相似的表达？已识别的蛋白质-蛋白质相互作用是否以前是通过其他方法检测到的？相互作用的蛋白质是否由具有相似表达谱和定位的基因编码？我们开发了 CORNET（用于相关网络）作为访问点，以获取拟南芥（Arabidopsis thaliana）的转录组、蛋白质互作组和定位数据以及功能信息。它由两个灵活且多功能的工具组成，即共表达工具和蛋白质-蛋白质相互作用工具。使用本体论术语浏览和搜索微阵列实验以及合并个人微阵列数据是微阵列存储库的独特功能。共表达工具允许交替或同时使用多种表达汇编，而蛋白质-蛋白质相互作用工具则搜索实验和计算确定的蛋白质-蛋白质相互作用。实施了不同的搜索选项，以构建以多个输入基因或蛋白质为中心的共表达和/或蛋白质-蛋白质相互作用网络。此外，网络和相关证据以 Cytoscape 可视化。本地化以饼图可视化，从而允许每个蛋白质具有多个本地化。CORNET 可在 http://bioinformatics.psb.ugent.be/cornet 上获得。
