Journal Article

Non-negative matrix factorization of gene expression profiles: a plug-in for BRB-ArrayTools

Qihao Qi, Yingdong Zhao, MingChung Li and Richard Simon

in Bioinformatics

Volume 25, issue 4, pages 545-547
Published in print February 2009 | ISSN: 1367-4803
Published online January 2009 | e-ISSN: 1460-2059 | DOI: http://dx.doi.org/10.1093/bioinformatics/btp009
Non-negative matrix factorization of gene expression profiles: a plug-in for BRB-ArrayTools

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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.

Contact: rsimon@mail.nih.gov

Journal Article.  1449 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology

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