title: BiologicalNetworks 2.0--an integrative view of genome biology data.
abstract: BACKGROUND
  A significant problem in the study of mechanisms of an organism's development is the elucidation of interrelated factors which are making an impact on the different levels of the organism, such as genes, biological molecules, cells, and cell systems. Numerous sources of heterogeneous data which exist for these subsystems are still not integrated sufficiently enough to give researchers a straightforward opportunity to analyze them together in the same frame of study. Systematic application of data integration methods is also hampered by a multitude of such factors as the orthogonal nature of the integrated data and naming problems.
  
  
  RESULTS
  Here we report on a new version of BiologicalNetworks, a research environment for the integral visualization and analysis of heterogeneous biological data. BiologicalNetworks can be queried for properties of thousands of different types of biological entities (genes/proteins, promoters, COGs, pathways, binding sites, and other) and their relations (interactions, co-expression, co-citations, and other). The system includes the build-pathways infrastructure for molecular interactions/relations and module discovery in high-throughput experiments. Also implemented in BiologicalNetworks are the Integrated Genome Viewer and Comparative Genomics Browser applications, which allow for the search and analysis of gene regulatory regions and their conservation in multiple species in conjunction with molecular pathways/networks, experimental data and functional annotations.
  
  
  CONCLUSIONS
  The new release of BiologicalNetworks together with its back-end database introduces extensive functionality for a more efficient integrated multi-level analysis of microarray, sequence, regulatory, and other data. BiologicalNetworks is freely available at http://www.biologicalnetworks.org.
authors.affiliation: San Diego Supercomputer Center, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.
authors.forename: Sergey
authors.initials: S
authors.lastname: Kozhenkov
authors.forename: Yulia
authors.initials: Y
authors.lastname: Dubinina
authors.forename: Mayya
authors.initials: M
authors.lastname: Sedova
authors.forename: Amarnath
authors.initials: A
authors.lastname: Gupta
authors.forename: Julia
authors.initials: J
authors.lastname: Ponomarenko
authors.forename: Michael
authors.initials: M
authors.lastname: Baitaluk
mesh_terms: D019295:Computational Biology / Q000379:methods; D003628:Database Management Systems; D030541:Databases, Genetic; D016678:Genome; D023281:Genomics / Q000379:methods*; D020407:Internet; D058977:Molecular Sequence Annotation; D020411:Oligonucleotide Array Sequence Analysis; D017422:Sequence Analysis, DNA