title: atBioNet--an integrated network analysis tool for genomics and biomarker discovery.
abstract: BACKGROUND
  Large amounts of mammalian protein-protein interaction (PPI) data have been generated and are available for public use. From a systems biology perspective, Proteins/genes interactions encode the key mechanisms distinguishing disease and health, and such mechanisms can be uncovered through network analysis. An effective network analysis tool should integrate different content-specific PPI databases into a comprehensive network format with a user-friendly platform to identify key functional modules/pathways and the underlying mechanisms of disease and toxicity.
  
  
  RESULTS
  atBioNet integrates seven publicly available PPI databases into a network-specific knowledge base. Knowledge expansion is achieved by expanding a user supplied proteins/genes list with interactions from its integrated PPI network. The statistically significant functional modules are determined by applying a fast network-clustering algorithm (SCAN: a Structural Clustering Algorithm for Networks). The functional modules can be visualized either separately or together in the context of the whole network. Integration of pathway information enables enrichment analysis and assessment of the biological function of modules. Three case studies are presented using publicly available disease gene signatures as a basis to discover new biomarkers for acute leukemia, systemic lupus erythematosus, and breast cancer. The results demonstrated that atBioNet can not only identify functional modules and pathways related to the studied diseases, but this information can also be used to hypothesize novel biomarkers for future analysis.
  
  
  CONCLUSIONS
  atBioNet is a free web-based network analysis tool that provides a systematic insight into proteins/genes interactions through examining significant functional modules. The identified functional modules are useful for determining underlying mechanisms of disease and biomarker discovery. It can be accessed at: http://www.fda.gov/ScienceResearch/BioinformaticsTools/ucm285284.htm.
authors: ICF International at FDA's National Center for Toxicological Research, Jefferson, AR 72079, USA.
authors: Yijun
authors: Y
authors: Ding
authors: Minjun
authors: M
authors: Chen
authors: Zhichao
authors: Z
authors: Liu
authors: Don
authors: D
authors: Ding
authors: Yanbin
authors: Y
authors: Ye
authors: Min
authors: M
authors: Zhang
authors: Reagan
authors: R
authors: Kelly
authors: Li
authors: L
authors: Guo
authors: Zhenqiang
authors: Z
authors: Su
authors: Stephen C
authors: SC
authors: Harris
authors: Feng
authors: F
authors: Qian
authors: Weigong
authors: W
authors: Ge
authors: Hong
authors: H
authors: Fang
authors: Xiaowei
authors: X
authors: Xu
authors: Weida
authors: W
authors: Tong
mesh_terms: D000465:Algorithms; D015415:Biomarkers / Q000378:metabolism*; D016000:Cluster Analysis; D030562:Databases, Protein; D023281:Genomics; D006801:Humans; D053858:Metabolic Networks and Pathways; D060066:Protein Interaction Maps; D012984:Software; D014584:User-Computer Interface
chemical_list: D015415:Biomarkers