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GenMAPP 2: New Features and Resources for Pathway Analysis
Biology Faculty Works
  • Nathan Salomonis, University of California - San Francisco
  • Kristina Hanspers, University of California - San Francisco
  • Alexander C Zambon, University of California - San Francisco
  • Karen Vranizan, University of California - San Francisco
  • Steven C Lawlor, University of California - San Francisco
  • Kam D Dahlquist, Loyola Marymount University
  • Scott W Doniger, Washington University School of Medicine in St. Louis
  • Josh Stuart, University of California - Santa Cruz
  • Bruce R Conklin, University of California - San Francisco
  • Alexander R Pico, University of California - San Francisco
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Background: Microarray technologies have evolved rapidly, enabling biologists to quantify genome-wide levels of gene expression, alternative splicing, and sequence variations for a variety of species. Analyzing and displaying these data present a significant challenge. Pathway-based approaches for analyzing microarray data have proven useful for presenting data and for generatingtestable hypotheses. Results: To address the growing needs of the microarray community we have released version 2 of Gene Map Annotator and Pathway Profiler (GenMAPP), a new GenMAPP database schema, and integrated resources for pathway analysis. We have redesigned the GenMAPP database to support multiple gene annotations and species as well as custom species database creation for a potentially unlimited number of species. We have expanded our pathway resources by utilizing homology information to translate pathway content between species and extending existing pathways with data derived from conserved protein interactions and coexpression. We have implemented a newmode of data visualization to support analysis of complex data, including time-course, single nucleotide polymorphism (SNP), and splicing. GenMAPP version 2 also offers innovative ways to display and share data by incorporating HTML export of analyses for entire sets of pathways as organized web pages. Conclusion: GenMAPP version 2 provides a means to rapidly interrogate complex experimental data for pathway-level changes in a diverse range of organisms.
Publisher Statement

© 2007 Salomonis et al; licensee BioMed Central Ltd.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Citation Information

Salomonis, N., Hanspers, K., Zambon, A.C., Vranizan, K., Lawlor, S.C., Dahlquist, K.D., Doniger, S.W., Stuart, J., Conklin, B.R., & Pico, A.R. (2007) GenMAPP 2: New Features and Resources for Pathway Analysis. BMC Bioinformatics 8: 217.