Visualization and analysis of 3D gene expression patterns in zebrafish using web services

D. Potikanond, F. Verbeek
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引用次数: 6

Abstract

The analysis of patterns of gene expression patterns analysis plays an important role in developmental biology and molecular genetics. Visualizing both quantitative and spatio-temporal aspects of gene expression patterns together with referenced anatomical structures of a model-organism in 3D can help identifying how a group of genes are expressed at a certain location at a particular developmental stage of an organism. In this paper, we present an approach to provide an online visualization of gene expression data in zebrafish (Danio rerio) within 3D reconstruction model of zebrafish in different developmental stages. We developed web services that provide programmable access to the 3D reconstruction data and spatial-temporal gene expression data maintained in our local repositories. To demonstrate this work, we develop a web application that uses these web services to retrieve data from our local information systems. The web application also retrieve relevant analysis of microarray gene expression data from an external community resource; i.e. the ArrayExpress Atlas. All the relevant gene expression patterns data are subsequently integrated with the reconstruction data of the zebrafish atlas using ontology based mapping. The resulting visualization provides quantitative and spatial information on patterns of gene expression in a 3D graphical representation of the zebrafish atlas in a certain developmental stage. To deliver the visualization to the user, we developed a Java based 3D viewer client that can be integrated in a web interface allowing the user to visualize the integrated information over the Internet.
利用web服务可视化和分析斑马鱼的三维基因表达模式
基因表达模式分析在发育生物学和分子遗传学中起着重要的作用。将基因表达模式的数量和时空方面以及模型生物的参考解剖结构在3D中可视化可以帮助识别一组基因如何在生物体的特定发育阶段的特定位置表达。在本文中,我们提出了一种方法,在斑马鱼不同发育阶段的三维重建模型中提供斑马鱼(Danio rerio)基因表达数据的在线可视化。我们开发了web服务,为本地存储库中保存的3D重建数据和时空基因表达数据提供可编程访问。为了演示这项工作,我们开发了一个web应用程序,该应用程序使用这些web服务从本地信息系统检索数据。该web应用程序还从外部社区资源检索微阵列基因表达数据的相关分析;即ArrayExpress Atlas。所有相关的基因表达模式数据随后使用基于本体的映射与斑马鱼图谱的重建数据集成。由此产生的可视化提供了在特定发育阶段的斑马鱼图谱的三维图形表示中基因表达模式的定量和空间信息。为了向用户提供可视化,我们开发了一个基于Java的3D查看器客户端,它可以集成在一个web界面中,允许用户通过Internet可视化集成的信息。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
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