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Molecular & Cellular Proteomics 2:1164-1176, 2003.
© 2003 by The American Society for Biochemistry and Molecular Biology, Inc.

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Research

PROTEOME-3D: An Interactive Bioinformatics Tool for Large-Scale Data Exploration and Knowledge Discovery^*

Deborah H. Lundgren, Jimmy Eng, Michael E. Wright and David K. Han^,¶

From the Center for Vascular Biology, Department of Physiology, University of Connecticut School of Medicine, Farmington, CT 06030, and Institute for Systems Biology, Seattle, WA 98103

Comprehensive understanding of biological systems requires efficient and systematic assimilation of high-throughput datasets in the context of the existing knowledge base. A major limitation in the field of proteomics is the lack of an appropriate software platform that can synthesize a large number of experimental datasets in the context of the existing knowledge base. Here, we describe a software platform, termed PROTEOME-3D, that utilizes three essential features for systematic analysis of proteomics data: creation of a scalable, queryable, customized database for identified proteins from published literature; graphical tools for displaying proteome landscapes and trends from multiple large-scale experiments; and interactive data analysis that facilitates identification of crucial networks and pathways. Thus, PROTEOME-3D offers a standardized platform to analyze high-throughput experimental datasets for the identification of crucial players in co-regulated pathways and cellular processes.

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