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KARMA: a web server application for comparing and annotating heterogeneous microarray platforms.

Kei-Hoi Cheung1, Janet Hager, Deyun Pan

  • 1Center for Medical Informatics, Department of Anesthesiology, Yale University, New Haven, CT, USA. kei.cheung@yale.edu

Nucleic Acids Research
|June 25, 2004
PubMed
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We developed KARMA, a web tool for comparing and annotating microarray platforms across species using genome data. This application aids researchers by identifying analogous DNA fragments for diverse array types.

Area of Science:

  • Bioinformatics
  • Genomics
  • Computational Biology

Background:

  • Microarray platform comparisons are essential for data integration and analysis.
  • Diverse genome annotation data from multiple sources pose challenges for cross-platform analysis.
  • Standardized tools are needed to facilitate the comparison of different microarray platforms.

Purpose of the Study:

  • To develop a universal web server application, KARMA, for comparing and annotating user-defined pairs of microarray platforms.
  • To enable cross-platform analysis using diverse genome annotation data across different species.
  • To provide a user-friendly interface for researchers to input and analyze microarray data.

Main Methods:

  • Developed a web server application (KARMA) for microarray platform comparison and annotation.

Related Experiment Videos

  • Utilized NCBI-Unigene identifiers for single-species comparisons and NCBI-Homologene data for cross-species comparisons.
  • Integrated diverse annotation data (LocusLink, SwissProt, Gene Ontology) from multiple sources into an Oracle database.

    • Main Results:

    • KARMA dynamically identifies analogous DNA fragments across multiple microarray platforms.
    • The application supports comparisons of diverse platforms, including commercial, custom, and resource-specific arrays.
    • Set operations (intersection, union, difference) are employed for single-species comparisons.

    Conclusions:

    • KARMA provides an effective tool for comparing and annotating diverse microarray platforms.
    • The application facilitates cross-species and single-species analyses using integrated genome annotation data.
    • KARMA enhances data accessibility and comparability for microarray research.