ArrayXPath: mapping and visualizing microarray gene-expression data with integrated biological pathway resources using Scalable Vector Graphics
ArrayXPath: mapping and visualizing microarray gene-expression data with integrated biological pathway resources using Scalable Vector Graphics
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DOI：
10.1093/nar/gkh476
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发表时间：
2004-07-01
影响因子：
14.9
通讯作者：
Kim, JH
中科院分区：
文献类型：
--
作者：
Chung, HJ;Kim, M;Kim, JH
生物途径可以提供生物系统组织的关键信息。ArrayXPath （http://www.snubi.org/software/ArrayXPath/）是一个基于web的服务，用于使用可缩放矢量图形（SVG）绘制和可视化集成生物途径资源的微阵列基因表达数据。通过整合主要的生物数据库和搜索路径资源，ArrayXPath可以自动从微阵列探针和路径元素中映射不同类型的标识符。当输入基因表达集群时，ArrayXPath为每个集群生成最佳匹配路径列表。我们应用Fisher精确检验和错误发现率（FDR）来评估集群和路径之间关联的统计显著性，同时纠正多重比较问题。ArrayXPath生成支持javascript的svg，用于支持web的与基因表达谱集成的路径的交互式可视化。
Biological pathways can provide key information on the organization of biological systems. ArrayXPath (http://www.snubi.org/software/ArrayXPath/) is a web-based service for mapping and visualizing microarray gene-expression data for integrated biological pathway resources using Scalable Vector Graphics (SVG). By integrating major bio-databases and searching pathway resources, ArrayXPath automatically maps different types of identifiers from microarray probes and pathway elements. When one inputs gene-expression clusters, ArrayXPath produces a list of the best matching pathways for each cluster. We applied Fisher's exact test and the false discovery rate (FDR) to evaluate the statistical significance of the association between a cluster and a pathway while correcting the multiple-comparison problem. ArrayXPath produces Javascript-enabled SVGs for web-enabled interactive visualization of pathways integrated with gene-expression profiles.