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ARROGANT: an application to manipulate large gene collections.

Amit V Kulkarni1, Noelle Sevilir Williams, Yun Lian

  • 1Program in Biomedical Engineering, The University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390, USA.

Bioinformatics (Oxford, England)
|November 9, 2002
PubMed
Summary

ARROGANT software aids in organizing gene and clone collections for efficient experimental design and data analysis. This tool facilitates the comparison of microarray data and gene annotation across diverse databases.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Managing and analyzing large-scale gene and clone collections from diverse databases presents significant challenges.
  • Efficiently comparing experimental data, particularly from microarrays, requires robust organizational tools.

Purpose of the Study:

  • To introduce ARROGANT (ARRay OrGANizing Tool), a software solution for organizing, annotating, and comparing extensive gene or clone datasets.
  • To enable users to compile and analyze gene collections from multiple sources for experimental design and data interpretation.

Main Methods:

  • ARROGANT utilizes the UniGene database to map disparate sequence identifiers to a common reference sequence.
  • The software facilitates the integration and comparison of gene expression data from various microarray experiments.

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  • It supports the annotation of genes on custom and commercial microarray platforms (e.g., Affymetrix).

    • Main Results:

    • Successfully applied ARROGANT to analyze colon cancer microarray expression data.
    • Utilized ARROGANT to compile candidate genes for cardiac diseases, aiding in single nucleotide polymorphism (SNP) discovery.
    • Employed ARROGANT in designing a novel human cDNA microarray for cancer research.
    • Demonstrated capability in combining and comparing expression data from different microarray platforms.

    Conclusions:

    • ARROGANT provides an efficient platform for managing and analyzing large gene/clone collections.
    • The tool enhances the ability to compare data across experiments and databases, supporting various genomic applications.
    • ARROGANT is a valuable asset for researchers in genomics, bioinformatics, and experimental design involving microarrays.