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A Web Tool for Generating High Quality Machine-readable Biological Pathways
Published on: February 8, 2017
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
Summary
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.
- 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.
