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BarleyBase--an expression profiling database for plant genomics.

Lishuang Shen1, Jian Gong, Rico A Caldo

  • 1Virtual Reality Applications Center, USDA-ARS, Iowa State University, Ames, IA 50011, USA.

Nucleic Acids Research
|December 21, 2004
PubMed
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BarleyBase is a comprehensive online database for plant microarray data, offering integrated tools for analysis and visualization. It facilitates cross-species comparisons and gene function prediction for researchers studying plant genomics.

Area of Science:

  • Plant genomics
  • Bioinformatics
  • Computational biology

Background:

  • Microarray technology generates large-scale gene expression data crucial for understanding plant biology.
  • Publicly available datasets require integrated platforms for efficient access, analysis, and interpretation.
  • Existing resources may lack comprehensive tools for cross-species comparative analysis.

Purpose of the Study:

  • To introduce BarleyBase (BB), an online database and analysis platform for plant microarray data.
  • To provide integrated tools for data visualization, statistical analysis, and querying.
  • To facilitate cross-species comparisons and gene function prediction.

Main Methods:

  • BB integrates raw and normalized expression data from Affymetrix genome arrays (Barley1, Arabidopsis ATH1, and planned additions).

Related Experiment Videos

  • The platform offers extensive query and display options across multiple data levels (experiments, hybridizations, probe sets, probes).
  • Cross-experiment queries incorporate expression profiles and biological information, linked with visualization and statistical analysis tools (e.g., R statistical toolbox).

    • Main Results:

    • BB provides access to diverse plant microarray datasets with advanced search functionalities.
    • Integrated tools enable detailed data exploration, including expression profiling and statistical analysis.
    • Links to external genomic resources (PlantGDB, Gramene, GrainGenes) support EST alignments and gene function prediction.

    Conclusions:

    • BarleyBase serves as a valuable, integrated resource for plant genomics research.
    • The platform enhances data accessibility, analysis capabilities, and cross-species comparative studies.
    • BB supports researchers in predicting gene function and advancing our understanding of plant genomes.