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. 2007 Feb 4:3:11-7.

Analysis of gene expression data using BRB-ArrayTools

Richard Simon  1 , Amy Lam, Ming-Chung Li, Michael Ngan, Supriya Menenzes, Yingdong Zhao
Affiliations

Analysis of gene expression data using BRB-ArrayTools

Richard Simon et al. Cancer Inform. .

Abstract

BRB-ArrayTools is an integrated software system for the comprehensive analysis of DNA microarray experiments. It was developed by professional biostatisticians experienced in the design and analysis of DNA microarray studies and incorporates methods developed by leading statistical laboratories. The software is designed for use by biomedical scientists who wish to have access to state-of-the-art statistical methods for the analysis of gene expression data and to receive training in the statistical analysis of high dimensional data. The software provides the most extensive set of tools available for predictive classifier development and complete cross-validation. It offers extensive links to genomic websites for gene annotation and analysis tools for pathway analysis. An archive of over 100 datasets of published microarray data with associated clinical data is provided and BRB-ArrayTools automatically imports data from the Gene Expression Omnibus public archive at the National Center for Biotechnology Information.

Keywords: Bioinformatics; biostatistics; gene expression; microarrays.

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Figures

Figure 1.
Figure 1.
Screen shot of BRB-ArrayTools pull-down menu in Microsoft Excel.
Figure 2.
Figure 2.
Screen shot of rotating 3-dimensional multidimensional scaling plot from BRB-ArrayTools. Each point represents a sample. The three axes are the first three principal components of the genes, representing the three dimensions of the expression profile of the samples having maximum variability. Samples are color coded by a characteristic selected by the user. In the case shown, the characteristic is presence of BRCA1 germline mutation (green), presence of BRCA2 germline mutation (red), or neither (blue). The direction and speed of rotation is controlled by the user. Points can be identified by clicking with mouse. The entire graphical display, including operating controls, can be automatically exported to Microsoft Powerpoint.
See this image and copyright information in PMC

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