title: PROTEOME-3D: an interactive bioinformatics tool for large-scale data exploration and knowledge discovery.
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.
authors.affiliation: Center for Vascular Biology, Department of Physiology, University of Connecticut School of Medicine, 263 Farmington Avenue, Farmington, CT 06030, USA.
authors.forename: Deborah H
authors.initials: DH
authors.lastname: Lundgren
authors.forename: Jimmy
authors.initials: J
authors.lastname: Eng
authors.forename: Michael E
authors.initials: ME
authors.lastname: Wright
authors.forename: David K
authors.initials: DK
authors.lastname: Han
mesh_terms: D019295:Computational Biology; D030562:Databases, Protein; D020407:Internet; D051188:Knowledge Bases; D040901:Proteomics; D020539:Sequence Analysis, Protein; D012984:Software