Cross-species microarray analysis with the OSCAR system suggests an INSR->Pax6->NQO1 neuro-protective pathway in aging and Alzheimer's disease.
Cross-species microarray analysis with the OSCAR system suggests an INSR->Pax6->NQO1 neuro-protective pathway in aging and Alzheimer's disease.
复制标题
与奥斯卡系统的跨物种微阵列分析表明，在衰老和阿尔茨海默氏病中，Insr-> pax6-> NQO1神经保护途径。
DOI：
10.1093/nar/gkm408
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发表时间：
2007-07
影响因子：
14.9
通讯作者：
Zhong, Sheng
中科院分区：
文献类型：
--
作者：
Lu, Yue;He, Xin;Zhong, Sheng
OSCAR是一个用于微阵列数据聚类和跨物种分析的网络平台。它为用户和算法开发人员提供了一个全面而友好的环境。对于用户，OSCAR提供了用于单物种和多物种数据的聚类工具，以及交互式分析功能。对于单物种数据，OSCAR目前提供了层次聚类，K-means，围绕中心点的分区（PAM），自组织映射（SOM），紧聚类和一种称为“共识紧聚类”的新算法。新的共识紧密聚类算法提供了强大的基因聚类，其结果比其他最先进的算法更能抵抗假阳性。对于跨物种数据分析，OSCAR提供了两个新的计算工具：“coherentsubset”和“coherentSubset”，以及一个新的可视化工具：“comparative heatmap”。将coherentCluster算法应用于人类和苍蝇的衰老数据，我们确定了几个相关的基因簇，它们共享与两个物种的衰老过程高度相关的协同调节模式。一个连贯的集群表明胰岛素受体（INSR）可能在两个物种和不同组织中调节Pax 6。对人脑表达和病理数据的进一步分析表明，INSR-> Pax 6->醌氧化还原酶（NQO 1）->解毒神经保护通路可能存在于衰老或患病的大脑中。对于算法开发人员来说，OSCAR是一个即插即用的平台。开发人员可以毫不费力地将自己的算法插入OSCAR服务器，而无需透露源代码，这将使其命令行可执行文件具有用户友好的界面和交互式分析功能。总之，OSCAR为聚类和跨物种分析程序的开发和应用提供了一个开放的平台。OSCAR是一个开放的微阵列数据聚类分析系统。可在以下网址获得：http://biocomp.bioen.uiuc.edu/oscar
OSCAR is a web platform for cluster and cross-species analysis of microarray data. It provides a comprehensive but friendly environment to both users and algorithm developers. For users, OSCAR provides cluster tools for both single and multiple species data, together with interactive analysis features. For single species data, OSCAR currently provides Hierarchical Clustering, K-means, partition around medoids (PAM), Self-Organizing Map (SOM), Tight Clustering and a novel algorithm called ‘Consensus Tight-clustering’. The new Consensus Tight-clustering algorithm delivers robust gene clusters and its result is more resistant to false positives than other state-of-the-art algorithms. For cross-species data analysis, OSCAR provides two novel computational tools: ‘coherentCluster’, ‘coherentSubset’ and a novel visualization tool: ‘comparative heatmap’. Applying the coherentCluster algorithm to human and fly aging data, we identified several coherent clusters of genes, which share co-regulation patterns that are highly correlated with the aging process in both of the two species. One coherent cluster suggests insulin receptor (INSR) may regulate Pax6 in both species and across different tissues. Further analysis with human brain expression and pathological data suggests an INSR->Pax6->quinone oxidoreductase (NQO1)->detoxification neuro-protective pathway might be present in aging or diseased brain. For algorithm developers, OSCAR is a plug-and-play platform. With little effort, developers can plug their own algorithms into the OSCAR server without revealing the source codes, which will equip their command line executables with user-friendly interface and interactive analysis capability. In summary, OSCAR initiates an open platform for development and application of clustering and cross-species analysis programs. OSCAR stands for an open system for cluster analysis of microarray data. It is available at: http://biocomp.bioen.uiuc.edu/oscar