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Data management and analysis for gene expression arrays

Nature Genetics volume 20, pages 19–23 (1998)Cite this article

Abstract

Microarray technology makes it possible to simultaneously study the expression of thousands of genes during a single experiment. We have developed an information system, ArrayDB, to manage and analyse large-scale expression data. The underlying relational database was designed to allow flexibility in the nature and structure of data input and also in the generation of standard or customized reports through a web-browser interface. ArrayDB provides varied options for data retrieval and analysis tools that should facilitate the interpretation of complex hybridization results. A sampling of ArrayDB storage, retrieval and analysis capabilities is available (http://www.nhgri.nih.gov/DIR/LCG/15K/HTML/), along with information on a set of approximately 15,000 genes used to fabricate several widely used microarrays. Information stored in ArrayDB is used to provide integrated gene expression reports by linking array target sequences with NCBI's Entrez retrieval system, UniGene and KEGG pathway views. The integration of external information resources is essential in interpreting intrinsic patterns and relationships in large-scale gene expression data.

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Figure 1: Cumulative growth of molecular biology and genetics literature (blue) compared with DNA sequences (green).
Figure 2: Schematic overview of the ArrayDB information management system.
Figure 3: Screen captures of various data retrieval and analysis tools within ArrayDB.
Figure 4: MultiExperiment viewer window.

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Acknowledgements

We thank M. Eisen, P. Brown and J. Hudson for stimulating discussions. We also thank J. Hudson and Research Genetics for re-arraying the 10K/15K clone sets from their original IMAGE cDNA libraries.

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Authors and Affiliations

  1. Cancer Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, 20892, Maryland, USA

    Olga Ermolaeva, Michael L. Bittner, Yidong Chen, Paul Meltzer & Jeffrey M. Trent

  2. National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, 20894, Maryland, USA

    Olga Ermolaeva, Kim D. Pruitt, Gregory D. Schuler & Mark S. Boguski

  3. Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, 20892, Maryland, USA

    Mohit Rastogi & Mark S. Boguski

  4. Biometric Research Branch, National Cancer Institute, National Institutes of Health, Bethesda, 20892, Maryland, USA

    Richard Simon

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  1. Olga Ermolaeva
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  2. Mohit Rastogi
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  3. Kim D. Pruitt
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  4. Gregory D. Schuler
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Correspondence to Mark S. Boguski.

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Ermolaeva, O., Rastogi, M., Pruitt, K. et al. Data management and analysis for gene expression arrays. Nat Genet 20, 19–23 (1998). https://doi.org/10.1038/1670

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