A Unified Expression Profiling Database for Plants and Plant Pathogens
  • Roger P. Wise
  • Rico A. Caldo
  • Lu Hong
  • Lishuang Shen
  • Ethalinda Cannon
  • Julie A. Dickerson
Part of the Methods in Molecular Biology™ book series (MIMB, volume 406)


BarleyBase ( and its successor, PLEXdb (, are public resources for large-scale gene expression analysis for plants and plant pathogens. BarleyBase/PLEXdb provides a unified web interface to support the functional interpretation of highly parallel microarray experiments integrated with traditional structural genomics and phenotypic data. Users can perform hypothesis building queries from multiple interlinked resources, e.g., a particular gene, a protein class, EST entries, and physical or genetic map position—all coupled to highly parallel gene expression, for a variety of crop and model plant species, from a large array of experimental or field conditions. Array data are interlinked to analytical and biological functions (e.g., Gene and Plant Ontologies, BLAST, spliced alignment, multiple alignment, regulatory motif identification, and expression analysis), allowing members of the community to access and analyze comparative expression experiments in conjunction with their own data.

Key Words

Expression profiling microarray MIAME plant ontology cluster analysis 



The authors thank Nick Lauter for critical review of the manuscript. BarleyBase/PLEXdb was initiated with funds from USDA-CSREES North American Barley Genome Project and is currently supported by USDA-National Research Initiative grant no. 02-35300-12619 and National Science Foundation Plant Genome grant no. 0500461 to RPW and JAD.vvsp-2


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Copyright information

© Humana Press Inc. 2007

Authors and Affiliations

  • Roger P. Wise
    • 1
  • Rico A. Caldo
    • 1
  • Lu Hong
    • 2
  • Lishuang Shen
    • 3
  • Ethalinda Cannon
    • 1
  • Julie A. Dickerson
    • 4
  1. 1.Corn Insects and Crop Genetics Research, USDA-ARS and Department of Plant Pathology and Center for Plant Responses to Environmental StressesIowa State UniversityAmes
  2. 2.Interdepartmental Bioinformatics & Computational BiologyIowa State UniversityAmes
  3. 3.Virtual Reality Applications CenterIowa State UniversityAmes
  4. 4.Virtual Reality Applications Center and Department of Electrical and Computer EngineeringIowa State UniversityAmes

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