基因表达谱的非负矩阵分解：BRB-ArrayTools的一个插件。
Non-negative matrix factorization of gene expression profiles: a plug-in for BRB-ArrayTools.
作者信息
Qi Qihao, Zhao Yingdong, Li MingChung, Simon Richard
机构信息
Department of Biochemistry and Molecular Biology, Georgetown University School of Medicine, 3900 Reservoir Rd. NW, Washington, DC 20057-1455, USA.
出版信息
Bioinformatics. 2009 Feb 15;25(4):545-7. doi: 10.1093/bioinformatics/btp009. Epub 2009 Jan 8.
SUMMARY
Non-negative matrix factorization (NMF) is an increasingly used algorithm for the analysis of complex high-dimensional data. BRB-ArrayTools is a widely used software system for the analysis of gene expression data with almost 9000 registered users in over 65 countries. We have developed a NMF analysis plug-in in BRB-ArrayTools for unsupervised sample clustering of microarray gene expression data. Our analysis tool also incorporates an algorithm for Semi-NMF which can handle both positive and negative elements for log-ratio data. Output includes a heat map of sample clusters and differentially expressed genes with extensive biological annotation. For comparison, output also includes the results of K-means clustering.
AVAILABILITY
The NMF analysis plug-in is freely available in BRB-ArrayTools for non-commercial users. BRB-ArrayTools can be downloaded at http://linus.nci.nih.gov/BRB-ArrayTools.html. The algorithms used for NMF and Semi-NMF are available at ftp://linus.nci.nih.gov/pub/NMF.
摘要
非负矩阵分解（NMF）是一种越来越多地用于分析复杂高维数据的算法。BRB-ArrayTools是一个广泛使用的用于分析基因表达数据的软件系统，在65个以上国家拥有近9000名注册用户。我们在BRB-ArrayTools中开发了一个NMF分析插件，用于对微阵列基因表达数据进行无监督样本聚类。我们的分析工具还集成了一种半NMF算法，该算法可以处理对数比数据的正元素和负元素。输出包括样本聚类热图和具有广泛生物学注释的差异表达基因。为了进行比较，输出还包括K均值聚类的结果。
可用性
NMF分析插件可在BRB-ArrayTools中免费提供给非商业用户。BRB-ArrayTools可从http://linus.nci.nih.gov/BRB-ArrayTools.html下载。用于NMF和半NMF的算法可从ftp://linus.nci.nih.gov/pub/NMF获得。
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