Graph-based analysis and visualization of experimental results with ONDEX
Graph-based analysis and visualization of experimental results with ONDEX
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DOI：
10.1093/bioinformatics/btl081
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发表时间：
2006-06-01
期刊：
影响因子：
5.8
通讯作者：
Philippi, Stephan
中科院分区：
文献类型：
--
作者：
Kohler, Jacob;Baumbach, Jan;Philippi, Stephan
动机：收集所需的相关信息来解释高通量，基因组规模，基因表达微阵列等实验的输出是具有挑战性的。分析显示基因在表达水平上显示统计学上显著的变化，但需要更多的信息来确定它们的生物学相关性。挑战在于将这些基因与分布在数百个数据库或埋藏在科学文献（数百万篇文章）中的生物信息结合起来。需要软件工具来自动化这项任务，目前这项任务是劳动密集型的，需要相当多的信息学和生物学专业知识。结果：本文描述了ONDEX及其如何应用于解释基因表达结果的任务。ONDEX是一个数据库系统，它结合了语义数据库集成和文本挖掘的特点以及基于图的分析方法。概述了ONDEX系统，重点介绍了最近开发的基于图形的分析和可视化功能。一个案例研究被用来展示ONDEX如何从基因表达数据中帮助识别应激反应基因和代谢途径之间的因果关系。ONDEX还发现了大多数基因的功能注释，这些注释在微阵列实验中表现出重要意义，但以前是未知的功能。
Motivation: Assembling the relevant information needed to interpret the output from high-throughput, genome scale, experiments such as gene expression microarrays is challenging. Analysis reveals genes that show statistically significant changes in expression levels, but more information is needed to determine their biological relevance. The challenge is to bring these genes together with biological information distributed across hundreds of databases or buried in the scientific literature (millions of articles). Software tools are needed to automate this task which at present is labor-intensive and requires considerable informatics and biological expertise.Results: This article describes ONDEX and how it can be applied to the task of interpreting gene expression results. ONDEX is a database system that combines the features of semantic database integration and text mining with methods for graph-based analysis. An overview of the ONDEX system is presented, concentrating on recently developed features for graph-based analysis and visualization. A case study is used to show how ONDEX can help to identify causal relationships between stress response genes and metabolic pathways from gene expression data. ONDEX also discovered functional annotations for most of the genes that emerged as significant in the microarray experiment, but were previously of unknown function.