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

Deborah H Lundgren; Jimmy Eng; Michael E Wright; David K Han

doi:10.1074/mcp.M300059-MCP200

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

Journal article

Open access

Peer reviewed

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

Molecular & cellular proteomics, Vol.2(11), pp.1164-1176

11/2003

DOI: 10.1074/mcp.M300059-MCP200

PMCID: PMC1487189

PMID: 12960178

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https://doi.org/10.1074/mcp.M300059-MCP200View

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Abstract

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.

Details

Title: Subtitle: PROTEOME-3D: An Interactive Bioinformatics Tool for Large-Scale Data Exploration and Knowledge Discovery
Creators: Deborah H Lundgren - From the Center for Vascular Biology, Department of Physiology, University of Connecticut School of Medicine, Farmington, CT 06030, and
Jimmy Eng - Institute for Systems Biology, Seattle, WA 98103
Michael E Wright - Institute for Systems Biology, Seattle, WA 98103
David K Han - From the Center for Vascular Biology, Department of Physiology, University of Connecticut School of Medicine, Farmington, CT 06030, and
Resource Type: Journal article
Publication Details: Molecular & cellular proteomics, Vol.2(11), pp.1164-1176
DOI: 10.1074/mcp.M300059-MCP200
PMID: 12960178
PMCID: PMC1487189
NLM abbreviation: Mol Cell Proteomics
ISSN: 1535-9476
eISSN: 1535-9484
Language: English
Date published: 11/2003
Academic Unit: Molecular Physiology and Biophysics
Record Identifier: 9984025334602771

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