BioNetwork Bench: Database and Software for Storage, Query, and Analysis of Gene and Protein Networks
Authors: Kohutyuk Oksana , Towfic Fadi , Greenlee M. Heather West , Honavar Vasant 
Published: November 2012

Gene and protein networks offer a powerful approach for integration of the disparate yet complimentary types of data that result from high-throughput analyses. Although many tools and databases are currently available for accessing such data, they are left unutilized by bench scientists as they generally lack features for effective analysis and integration of both public and private datasets and do not offer an intuitive interface for use by scientists with limited computational expertise. We describe BioNetwork Bench, an open source, user-friendly suite of database and software tools for constructing, querying, and analyzing gene and protein network models. It enables biologists to analyze public as well as private gene expression; interactively query gene expression datasets; integrate data from multiple networks; store and selectively share the data and results. Finally, we describe an application of BioNetwork Bench to the assembly and iterative expansion of a gene network that controls the differentiation of retinal progenitor cells into rod photoreceptors. The tool is available from http://bionetworkbench.sourceforge.net/ Background The emergence of high-throughput technologies has allowed many biological investigators to collect a great deal of information about the behavior of genes and gene products over time or during a particular disease state. Gene and protein networks offer a powerful approach for integration of the disparate yet complimentary types of data that result from such high-throughput analyses. There are a growing number of public databases, as well as tools for visualization and analysis of networks. However, such databases and tools have yet to be widely utilized by bench scientists, as they generally lack features for effective analysis and integration of both public and private datasets and do not offer an intuitive interface for use by biological scientists with limited computational expertise. Results We describe BioNetwork Bench, an open source, user-friendly suite of database and software tools for constructing, querying, and analyzing gene and protein network models. BioNetwork Bench currently supports a broad class of gene and protein network models (eg, weighted and un-weighted, undirected graphs, multi-graphs). It enables biologists to analyze public as well as private gene expression, macromolecular interaction and annotation data; interactively query gene expression datasets; integrate data from multiple networks; query multiple networks for interactions of interest; store and selectively share the data as well as results of analyses. BioNetwork Bench is implemented as a plug-in for, and hence is fully interoperable with, Cytoscape, a popular open-source software suite for visualizing macromolecular interaction networks. Finally, we describe an application of BioNetwork Bench to the problem of assembly and iterative expansion of a gene network that controls the differentiation of retinal progenitor cells into rod photoreceptors. Conclusions BioNetwork Bench provides a suite of open source software for construction, querying, and selective sharing of gene and protein networks. Although initially aimed at a community of biologists interested in retinal development, the tool can be adapted easily to work with other biological systems simply by populating the associated database with the relevant datasets.