MOVE: A Multi-level Ontology-based Visualization and Exploration framework for genomic networks
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Date
2006
Journal Title
Journal ISSN
Volume Title
Publisher
Silico Biology
Abstract
Among the various research areas that comprise bioinformatics, systems biology is gaining increasing
attention. An important goal of systems biology is the unraveling of dynamic interactions between
components of living cells (e. g., proteins, genes). These interactions exist among others on genomic,
transcriptomic, proteomic and metabolomic levels. The levels themselves are heavily interconnected,
resulting in complex networks of different interacting biological entities. Currently, various
bioinformatics tools exist which are able to perform a particular analysis on a particular type of network.
Unfortunately, each tool has its own disadvantages hampering it to be used consistently for different
types of networks or analytical methods. This paper describes the conceptual development of an open
source extensible software framework that supports visualization and exploration of highly complex
genomic networks, like metabolic or gene regulatory networks. The focus is on the conceptual
foundations, starting from requirements, a description of the state of the art of network visualization
systems, and an analysis of their shortcomings. We describe the implementation of some initial
modules of the framework and apply them to a biological test case in bacterial regulation, which shows
the relevance and feasibility of the proposed approach.
Description
Keywords
Gene regulatory networks, Prokaryotes, Visualization framework, Information exploration
Citation
Bosman, D. W., Blom, E. J., Ogao, P. J., Kuipers, O. P., & Roerdink, J. B. T. M. (2006). MOVE: A multi-level ontology-based visualization and exploration framework for genomic networks. Silico Biology, 7(0004).