Visualizing Domain Interaction Networks and the Impact of Alternative Splicing Events

IF 1.3 Q4 ENGINEERING, BIOMEDICAL

Computer Methods in Biomechanics and Biomedical Engineering-Imaging and Visualization Pub Date : 2008-07-09 DOI:10.1109/MEDIVIS.2008.16

D. Emig, K. Klein, A. Kunert, Petra Mutzel, M. Albrecht

引用次数: 2

Abstract

In recent years, comprehensive studies of protein and domain networks have produced large amounts of interaction data. Further work has revealed that alternative splicing is a major cause of the observed protein and interaction diversity. Special microarrays now allow for measuring gene expression at the exon level, which enables the identification of alternative splicing events. We developed the Cytoscape plugin DomainGraph that facilitates the construction and visualization of protein and domain interaction networks. This plugin additionally supports the integration of exon expression data to highlight the effects of alternative splicing on the networks. We also designed and implemented a radial layout algorithm that specifically takes the integrated biological information for the networks into account and improves the visual presentation of the protein domain graphs considerably.

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可视化领域交互网络和可选剪接事件的影响

近年来，对蛋白质和结构域网络的全面研究产生了大量的相互作用数据。进一步的研究表明，选择性剪接是观察到的蛋白质和相互作用多样性的主要原因。特殊的微阵列现在允许在外显子水平上测量基因表达，从而能够识别备选剪接事件。我们开发了Cytoscape插件DomainGraph，促进了蛋白质和结构域相互作用网络的构建和可视化。该插件还支持外显子表达数据的集成，以突出显示网络上的替代剪接的影响。我们还设计并实现了一种径向布局算法，该算法特别考虑了网络的综合生物信息，并大大改善了蛋白质结构域图的视觉呈现。

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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来源期刊

Computer Methods in Biomechanics and Biomedical Engineering-Imaging and Visualization ENGINEERING, BIOMEDICAL-

CiteScore

2.80

自引率

6.20%

发文量

102

期刊介绍： Computer Methods in Biomechanics and Biomedical Engineering: Imaging & Visualization is an international journal whose main goals are to promote solutions of excellence for both imaging and visualization of biomedical data, and establish links among researchers, clinicians, the medical technology sector and end-users. The journal provides a comprehensive forum for discussion of the current state-of-the-art in the scientific fields related to imaging and visualization, including, but not limited to: Applications of Imaging and Visualization Computational Bio- imaging and Visualization Computer Aided Diagnosis, Surgery, Therapy and Treatment Data Processing and Analysis Devices for Imaging and Visualization Grid and High Performance Computing for Imaging and Visualization Human Perception in Imaging and Visualization Image Processing and Analysis Image-based Geometric Modelling Imaging and Visualization in Biomechanics Imaging and Visualization in Biomedical Engineering Medical Clinics Medical Imaging and Visualization Multi-modal Imaging and Visualization Multiscale Imaging and Visualization Scientific Visualization Software Development for Imaging and Visualization Telemedicine Systems and Applications Virtual Reality Visual Data Mining and Knowledge Discovery.