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Bioinformatics Advance Access published online on January 8, 2009
Bioinformatics, doi:10.1093/bioinformatics/btp009
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Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

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

Qihao Qi 1, Yingdong Zhao 2, MingChung Li 3 and Richard Simon 2,*

1Department of Biochemistry and Molecular Biology, Georgetown University School of Medicine, 3900 Reservoir Rd. NW, Washington, DC 20057-1455, USA
2Biometric Research Branch, National Cancer Institute, 9000 Rockville Pike, Bethesda, MD 20892-7434, USA
3The EMMES Corporation, Rockville, MD 20850, USA

*To whom correspondence should be addressed. Richard Simon, E-mail: rsimon{at}mail.nih.gov


  Abstract

Summary: Nonnegative matrix factorization (NMF) is an increas-ingly used algorithm which requires all elements in matrix are nonnegative 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-Nonnegative matrix factorization 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 nonnegative matrix factorization 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.

Contact: rsimon{at}mail.nih.gov

Associate Editor: Dr. Joaquin Dopazo

Received on September 8, 2008; revised on October 23, 2008; accepted on January 1, 2009

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