Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York 10003, USA.
Plant Physiol. 2010 Feb;152(2):500-15. doi: 10.1104/pp.109.147025. Epub 2009 Dec 9.
Data generation is no longer the limiting factor in advancing biological research. In addition, data integration, analysis, and interpretation have become key bottlenecks and challenges that biologists conducting genomic research face daily. To enable biologists to derive testable hypotheses from the increasing amount of genomic data, we have developed the VirtualPlant software platform. VirtualPlant enables scientists to visualize, integrate, and analyze genomic data from a systems biology perspective. VirtualPlant integrates genome-wide data concerning the known and predicted relationships among genes, proteins, and molecules, as well as genome-scale experimental measurements. VirtualPlant also provides visualization techniques that render multivariate information in visual formats that facilitate the extraction of biological concepts. Importantly, VirtualPlant helps biologists who are not trained in computer science to mine lists of genes, microarray experiments, and gene networks to address questions in plant biology, such as: What are the molecular mechanisms by which internal or external perturbations affect processes controlling growth and development? We illustrate the use of VirtualPlant with three case studies, ranging from querying a gene of interest to the identification of gene networks and regulatory hubs that control seed development. Whereas the VirtualPlant software was developed to mine Arabidopsis (Arabidopsis thaliana) genomic data, its data structures, algorithms, and visualization tools are designed in a species-independent way. VirtualPlant is freely available at www.virtualplant.org.
数据生成不再是推进生物研究的限制因素。此外，数据的整合、分析和解释已成为基因组研究的生物学家每天面临的关键瓶颈和挑战。为了使生物学家能够从不断增加的基因组数据中得出可测试的假设，我们开发了 VirtualPlant 软件平台。VirtualPlant 使科学家能够从系统生物学的角度可视化、整合和分析基因组数据。VirtualPlant 集成了有关基因、蛋白质和分子之间已知和预测关系的全基因组数据，以及基因组规模的实验测量数据。VirtualPlant 还提供可视化技术，以可视化格式呈现多变量信息，便于提取生物学概念。重要的是，VirtualPlant 帮助没有计算机科学背景的生物学家挖掘基因列表、微阵列实验和基因网络，以解决植物生物学中的问题，例如：内部或外部干扰如何影响控制生长和发育的过程？我们通过三个案例研究说明了 VirtualPlant 的使用，从查询感兴趣的基因到识别控制种子发育的基因网络和调节枢纽。虽然 VirtualPlant 软件是为挖掘拟南芥（Arabidopsis thaliana）基因组数据而开发的，但它的数据结构、算法和可视化工具是以与物种无关的方式设计的。VirtualPlant 可在 www.virtualplant.org 上免费获得。
