title: VisANT: an online visualization and analysis tool for biological interaction data.
abstract: BACKGROUND
  New techniques for determining relationships between biomolecules of all types--genes, proteins, noncoding DNA, metabolites and small molecules--are now making a substantial contribution to the widely discussed explosion of facts about the cell. The data generated by these techniques promote a picture of the cell as an interconnected information network, with molecular components linked with one another in topologies that can encode and represent many features of cellular function. This networked view of biology brings the potential for systematic understanding of living molecular systems.
  
  
  RESULTS
  We present VisANT, an application for integrating biomolecular interaction data into a cohesive, graphical interface. This software features a multi-tiered architecture for data flexibility, separating back-end modules for data retrieval from a front-end visualization and analysis package. VisANT is a freely available, open-source tool for researchers, and offers an online interface for a large range of published data sets on biomolecular interactions, including those entered by users. This system is integrated with standard databases for organized annotation, including GenBank, KEGG and SwissProt. VisANT is a Java-based, platform-independent tool suitable for a wide range of biological applications, including studies of pathways, gene regulation and systems biology.
  
  
  CONCLUSIONS
  VisANT has been developed to provide interactive visual mining of biological interaction data sets. The new software provides a general tool for mining and visualizing such data in the context of sequence, pathway, structure, and associated annotations. Interaction and predicted association data can be combined, overlaid, manipulated and analyzed using a variety of built-in functions. VisANT is available at http://visant.bu.edu.
authors.affiliation: Bioinformatics Program, Boston University, Boston, MA 02215, USA. zjhu@bu.edu
authors.forename: Zhenjun
authors.initials: Z
authors.lastname: Hu
authors.forename: Joseph
authors.initials: J
authors.lastname: Mellor
authors.forename: Jie
authors.initials: J
authors.lastname: Wu
authors.forename: Charles
authors.initials: C
authors.lastname: DeLisi
mesh_terms: D000818:Animals; D019295:Computational Biology / Q000379:methods*; D003196:Computer Graphics / Q000639:trends*; D003628:Database Management Systems / Q000706:statistics & numerical data; D030541:Databases, Genetic / Q000706:statistics & numerical data; D020869:Gene Expression Profiling / Q000706:statistics & numerical data; D005786:Gene Expression Regulation / Q000502:physiology; D005800:Genes, Fungal / Q000235:genetics; D017238:Genes, Helminth / Q000235:genetics; D015801:Helminth Proteins / Q000235:genetics; D006801:Humans; D051379:Mice; D025941:Protein Interaction Mapping / Q000706:statistics & numerical data; D012441:Saccharomyces cerevisiae / Q000235:genetics; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics; D012984:Software; D012985:Software Design; D014157:Transcription Factors / Q000235:genetics; D014158:Transcription, Genetic / Q000502:physiology; D020798:Two-Hybrid System Techniques / Q000706:statistics & numerical data
chemical_list: D015801:Helminth Proteins; D029701:Saccharomyces cerevisiae Proteins; D014157:Transcription Factors