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Related Experiment Videos

GenMAPP 2: new features and resources for pathway analysis.

Nathan Salomonis1, Kristina Hanspers, Alexander C Zambon

  • 1Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA. nsalomonis@gladstone.ucsf.edu <nsalomonis@gladstone.ucsf.edu>

BMC Bioinformatics
|June 26, 2007
PubMed
Summary
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GenMAPP version 2 enhances pathway analysis for gene expression data. This updated tool supports multiple species and complex data types, facilitating rapid discovery of pathway-level changes.

Area of Science:

  • Bioinformatics
  • Genomics
  • Systems Biology

Background:

  • Microarray technology enables genome-wide gene expression, splicing, and variation analysis.
  • Analyzing and visualizing complex microarray data remains a significant challenge.
  • Pathway-based approaches are valuable for data interpretation and hypothesis generation.

Purpose of the Study:

  • To release version 2 of Gene Map Annotator and Pathway Profiler (GenMAPP) with an updated database schema and integrated pathway analysis resources.
  • To enhance capabilities for analyzing diverse and complex genomic datasets.
  • To improve the sharing and visualization of pathway analysis results.

Main Methods:

  • Redesigned GenMAPP database to support multiple gene annotations and species, including custom databases.

Related Experiment Videos

  • Expanded pathway resources using homology information for cross-species translation and conserved interactions.
  • Implemented new data visualization modes for time-course, SNP, and splicing data.
  • Incorporated HTML export for organized web page display of pathway analyses.

    • Main Results:

    • GenMAPP version 2 supports an unlimited number of species and custom databases.
    • Pathway content is translatable across species, extending existing pathways with new data.
    • New visualization modes facilitate analysis of complex experimental data.
    • HTML export enables organized sharing of pathway analysis results.

    Conclusions:

    • GenMAPP version 2 enables rapid interrogation of complex experimental data for pathway-level changes.
    • The tool supports pathway analysis across a diverse range of organisms.
    • Facilitates hypothesis generation and data interpretation in genomics research.