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GECKO: a complete large-scale gene expression analysis platform.

Joachim Theilhaber1, Anatoly Ulyanov, Anish Malanthara

  • 1Cambridge Genomics Center, Sanofi-Aventis, 26 Landsdowne Street, Cambridge, MA 02139, USA. joachim.theilhaber@aventis.com

BMC Bioinformatics
|December 14, 2004
PubMed
Summary

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Gecko is a centralized gene expression analysis system designed for distributed communities. Its client-server architecture and Analysis Tree facilitate complex data sharing and analysis for numerous users.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Gecko (Gene Expression: Computation and Knowledge Organization) is a centralized system addressing the needs of distributed scientific communities.
  • It provides a high-capacity platform for gene expression analysis.

Purpose of the Study:

  • To develop and present a comprehensive gene expression analysis system.
  • To support a large, distributed user community in analyzing complex biological data.

Main Methods:

  • Utilizes a client-server architecture with a centralized data repository.
  • Incorporates automatic data processing pipelines, a database, and a computational engine with approximately 50 analysis tools.
  • Features an Analysis Tree (directed acyclic graph) for saving successive analytical results.

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Main Results:

  • The system handles tens of thousands of Affymetrix scans and offers diverse analysis tools like clustering, PCA, and ANOVA.
  • Its open architecture allows integration of new algorithms and analysis of non-gene expression data.
  • The Analysis Tree enables efficient sharing and revisiting of complex analyses for a large user base (approx. 100 users).

Conclusions:

  • The Gecko system is publicly available as free software.
  • Its flexible framework is suitable for users and developers with diverse analysis requirements.