title: BiologicalNetworks: visualization and analysis tool for systems biology.
abstract: 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 http://brak.sdsc.edu/pub/BiologicalNetworks.
authors.affiliation: San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA. baitaluk@sdsc.edu
authors.forename: Michael
authors.initials: M
authors.lastname: Baitaluk
authors.forename: Mayya
authors.initials: M
authors.lastname: Sedova
authors.forename: Animesh
authors.initials: A
authors.lastname: Ray
authors.forename: Amarnath
authors.initials: A
authors.lastname: Gupta
mesh_terms: D003196:Computer Graphics; D030541:Databases, Genetic; D020869:Gene Expression Profiling; D023281:Genomics / Q000379:methods*; D020407:Internet; D020411:Oligonucleotide Array Sequence Analysis; D012984:Software; D049490:Systems Biology / Q000379:methods*; D018511:Systems Integration; D014584:User-Computer Interface