title: Tissue-specific subnetworks and characteristics of publicly available human protein interaction databases.
abstract: BACKGROUND
  Protein-protein interaction (PPI) databases are widely used tools to study cellular pathways and networks; however, there are several databases available that still do not account for cell type-specific differences. Here, we evaluated the characteristics of six interaction databases, incorporated tissue-specific gene expression information and finally, investigated if the most popular proteins of scientific literature are involved in good quality interactions.
  
  
  RESULTS
  We found that the evaluated databases are comparable in terms of node connectivity (i.e. proteins with few interaction partners also have few interaction partners in other databases), but may differ in the identity of interaction partners. We also observed that the incorporation of tissue-specific expression information significantly altered the interaction landscape and finally, we demonstrated that many of the most intensively studied proteins are engaged in interactions associated with low confidence scores. In summary, interaction databases are valuable research tools but may lead to different predictions on interactions or pathways. The accuracy of predictions can be improved by incorporating datasets on organ- and cell type-specific gene expression, and by obtaining additional interaction evidence for the most 'popular' proteins.
  
  
  BACKGROUND
  kitano@sbi.jp
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: JST ERATO KAWAOKA Infection-induced Host Responses Project, Tokyo, Japan.
authors.forename: Tiago J S
authors.initials: TJ
authors.lastname: Lopes
authors.forename: Martin
authors.initials: M
authors.lastname: Schaefer
authors.forename: Jason
authors.initials: J
authors.lastname: Shoemaker
authors.forename: Yukiko
authors.initials: Y
authors.lastname: Matsuoka
authors.forename: Jean-Fred
authors.initials: JF
authors.lastname: Fontaine
authors.forename: Gabriele
authors.initials: G
authors.lastname: Neumann
authors.forename: Miguel A
authors.initials: MA
authors.lastname: Andrade-Navarro
authors.forename: Yoshihiro
authors.initials: Y
authors.lastname: Kawaoka
authors.forename: Hiroaki
authors.initials: H
authors.lastname: Kitano
mesh_terms: D030562:Databases, Protein; D015870:Gene Expression; D006801:Humans; D025941:Protein Interaction Mapping; D011506:Proteins / Q000235:genetics / Q000378:metabolism
chemical_list: D011506:Proteins