Reactome pathway analysis to enrich biological discovery in proteomics data sets.
Reactome pathway analysis to enrich biological discovery in proteomics data sets.
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DOI：
10.1002/pmic.201100066
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发表时间：
2011-09
期刊：
影响因子：
3.4
通讯作者：
Stein L
中科院分区：
文献类型：
--
作者：
Haw R;Hermjakob H;D'Eustachio P;Stein L
Reactome(http://www.reactome.org)是一个开源的、专家创作的、同行评审的、手动管理的反应、途径和生物过程数据库。我们为路径知识提供了一个直观的基于Web的用户界面和一套数据分析工具。路径浏览器是一种类似系统生物学图形符号(SBGN)的可视化系统，它通过缩放、滚动和事件突出显示来支持路径的手动导航，并利用PSI通用查询接口(PSIQUIC)网络服务将路径与来自反应组功能相互作用(FI)网络和相互作用数据库(如完整、ChEMBL和BioGRID)的分子相互作用数据覆盖在一起。路径和表达分析工具使用Web服务来提供ID映射、路径分配和用户提供的数据集的过度表示分析。通过将EnSembl比较应用于经过策划的人类蛋白质和反应，Reactome为其他20个物种产生了路径推断。物种比较工具以表格的形式提供每个物种的结果摘要，显示通过路径找到的同源蛋白质的数量，用户可以从该路径导航到特定蛋白质和反应的推断细节。Reactome多样化的途径知识和数据分析工具套件为大规模蛋白质组学数据集的数据挖掘、建模和分析提供了一个平台。
Reactome (http://www.reactome.org) is an open source, expert-authored, peer-reviewed, manually curated database of reactions, pathways and biological processes. We provide an intuitive web-based user interface to pathway knowledge and a suite of data analysis tools. The Pathway Browser is a Systems Biology Graphical Notation (SBGN)-like visualization system that supports manual navigation of pathways by zooming, scrolling and event highlighting, and that exploits PSI Common Query Interface (PSIQUIC) web services to overlay pathways with molecular interaction data from the Reactome Functional Interaction (FI) Network and interaction databases such as IntAct, ChEMBL, and BioGRID. Pathway and Expression Analysis tools employ web services to provide ID mapping, pathway assignment and over-representation analysis of user-supplied datasets. By applying Ensembl Compara to curated human proteins and reactions, Reactome generates pathway inferences for 20 other species. The Species Comparison tool provides a summary of results for each of these species as a table showing numbers of orthologous proteins found by pathway from which users can navigate to inferred details for specific proteins and reactions. Reactome’s diverse pathway knowledge and suite of data analysis tools provide a platform for data mining, modeling and the analysis of large-scale proteomics datasets.