BiologicalNetworks: visualization and analysis tool for systems biology

Systems level investigation of genomic scale information requires the development of truly integrated databases dealing with heterogeneous data, which can be queried for simple properties of genes or other database objects as well as for complex network level properties, for the analysis and modelling of complex biological processes. Towards that goal, we recently constructed PathSys, a data integration platform for systems biology, which provides dynamic integration over a diverse set of databases [Baitaluk et al. (2006) BMC Bioinformatics 7, 55]. Here we describe a server, BiologicalNetworks, which provides visualization, analysis services and an information management framework over PathSys. The server allows easy retrieval, construction and visualization of complex biological networks, including genome-scale integrated networks of protein–protein, protein–DNA and genetic interactions. Most importantly, BiologicalNetworks addresses the need for systematic presentation and analysis of high-throughput expression data by mapping and analysis of expression profiles of genes or proteins simultaneously on to regulatory, metabolic and cellular networks. BiologicalNetworks Server is available at .

[1]  P. Shannon,et al.  Cytoscape: a software environment for integrated models of biomolecular interaction networks. , 2003, Genome research.

[2]  C. Sander,et al.  The HUPO PSI's Molecular Interaction format—a community standard for the representation of protein interaction data , 2004, Nature Biotechnology.

[3]  Jihoon Kim,et al.  ArrayXPath: mapping and visualizing microarray gene-expression data with integrated biological pathway resources using Scalable Vector Graphics , 2004, Nucleic Acids Res..

[4]  Ian M. Donaldson,et al.  BIND: the Biomolecular Interaction Network Database , 2001, Nucleic Acids Res..

[5]  Frank Schacherer,et al.  The TRANSPATH signal transduction database: a knowledge base on signal transduction networks , 2001, Bioinform..

[6]  Shoshana J. Wodak,et al.  From Molecular Activities and Processes to Biological Function , 2001, Briefings Bioinform..

[7]  Zhenjun Hu,et al.  VisANT: an online visualization and analysis tool for biological interaction data , 2004, BMC Bioinformatics.

[8]  Kei-Hoi Cheung,et al.  PathMAPA: a tool for displaying gene expression and performing statistical tests on metabolic pathways at multiple levels for Arabidopsis , 2003, BMC Bioinformatics.

[9]  Gene Ontology Consortium.  The Gene Ontology (GO) database and informatics resource , 2003 .

[10]  Sergei Egorov,et al.  Pathway studio - the analysis and navigation of molecular networks , 2003, Bioinform..

[11]  Zhenjun Hu,et al.  VisANT: data-integrating visual framework for biological networks and modules , 2005, Nucleic Acids Res..

[12]  Robert Giegerich,et al.  PathFinder: reconstruction and dynamic visualization of metabolic pathways , 2002, Bioinform..

[13]  Hubert Hackl,et al.  PathwayExplorer: web service for visualizing high-throughput expression data on biological pathways , 2005, Nucleic Acids Res..

[14]  Amarnath Gupta,et al.  PathSys: integrating molecular interaction graphs for systems biology , 2006, BMC Bioinformatics.

[15]  Katherine C. Chen,et al.  Integrative analysis of cell cycle control in budding yeast. , 2004, Molecular biology of the cell.

[16]  David W. Mount,et al.  Pathway Miner: extracting gene association networks from molecular pathways for predicting the biological significance of gene expression microarray data , 2004, Bioinform..

[17]  Gultekin Özsoyoglu,et al.  Pathways Database System: An Integrated System for Biological Pathways , 2003, Bioinform..

[18]  M. Tyers,et al.  Osprey: a network visualization system , 2003, Genome Biology.

[19]  Hiroyuki Ogata,et al.  KEGG: Kyoto Encyclopedia of Genes and Genomes , 1999, Nucleic Acids Res..

[20]  A. Brazma,et al.  Towards reconstruction of gene networks from expression data by supervised learning , 2003, Genome Biology.

[21]  Kara Dolinski,et al.  Saccharomyces Genome Database provides tools to survey gene expression and functional analysis data , 2001, Nucleic Acids Res..

[22]  Hiroaki Kitano,et al.  The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models , 2003, Bioinform..