title: Modularity analysis based on predicted protein-protein interactions provides new insights into pathogenicity and cellular process of Escherichia coli O157:H7.
abstract: BACKGROUND
  With the development of experimental techniques and bioinformatics, the quantity of data available from protein-protein interactions (PPIs) is increasing exponentially. Functional modules can be identified from protein interaction networks. It follows that the investigation of functional modules will generate a better understanding of cellular organization, processes, and functions. However, experimental PPI data are still limited, and no modularity analysis of PPIs in pathogens has been published to date.
  
  
  RESULTS
  In this study, we predict and analyze the functional modules of E. coli O157:H7 systemically by integrating several bioinformatics methods. After evaluation, most of the predicted modules are found to be biologically significant and functionally homogeneous. Six pathogenicity-related modules were discovered and analyzed, including novel modules. These modules provided new information on the pathogenicity of O157:H7. The modularity of cellular function and cooperativity between modules are also discussed. Moreover, modularity analysis of O157:H7 can provide possible candidates for biological pathway extension and clues for discovering new pathways of cross-talk.
  
  
  CONCLUSIONS
  This article provides the first modularity analysis of a pathogen and sheds new light on the study of pathogens and cellular processes. Our study also provides a strategy for applying modularity analysis to any sequenced organism.
authors.affiliation: State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, Beijing 100071, China.
authors.forename: Xia
authors.initials: X
authors.lastname: Wang
authors.forename: Junjie
authors.initials: J
authors.lastname: Yue
authors.forename: Xianwen
authors.initials: X
authors.lastname: Ren
authors.forename: Yuelan
authors.initials: Y
authors.lastname: Wang
authors.forename: Mingfeng
authors.initials: M
authors.lastname: Tan
authors.forename: Beiping
authors.initials: B
authors.lastname: Li
authors.forename: Long
authors.initials: L
authors.lastname: Liang
mesh_terms: D017124:Conserved Sequence; D030562:Databases, Protein; D019453:Escherichia coli O157 / Q000166:cytology* / Q000378:metabolism / Q000472:pathogenicity*; D029968:Escherichia coli Proteins / Q000378:metabolism*; D058977:Molecular Sequence Annotation; D046912:Multiprotein Complexes / Q000378:metabolism; D060066:Protein Interaction Maps; D017386:Sequence Homology, Amino Acid
chemical_list: D029968:Escherichia coli Proteins; D046912:Multiprotein Complexes