title: Introduction of inflammatory bowel disease biomarkers panel using protein-protein interaction (PPI) network analysis.
abstract: OBJECTIVE
  In the present study, a protein-protein interaction network construction is conducted for IBD.
  
  
  BACKGROUND
  Inflammatory bowel diseases as serious chronic gastrointestinal disorders attracted many molecular investigations. Diverse molecular information is present for IBD. However, these molecular findings are not highlighted based on interactome analysis. On the other hand, PPI network analysis is a powerful method for study of molecular interactions in the protein level that provide useful information for highlighting the desired key proteins.
  
  
  METHODS
  Cytoscape is the used software with its plug-ins for detailed analysis. Two centrality parameters including degree and betweenness are determined and the crucial proteins based on these parameters are introduced.
  
  
  RESULTS
  The 75 proteins among 100 initial proteins are included in the network of IBD. Seventy-five nodes and 260 edges constructed the network as a scale free network. The findings indicate that there are seven hub-bottleneck proteins in the IBD network.
  
  
  CONCLUSIONS
  More examination revealed the essential roles of these key proteins in the integrity of the network. Finally, the indicator panel including NFKB1, CD40, TNFA, TYK2, NOD2, IL23R, and STAT3 is presented as a possible molecular index for IBD.
authors.affiliation: Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
authors.forename: Hamid
authors.initials: H
authors.lastname: Asadzadeh-Aghdaee
authors.affiliation: Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
authors.forename: Shabnam
authors.initials: S
authors.lastname: Shahrokh
authors.affiliation: Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
authors.forename: Mohsen
authors.initials: M
authors.lastname: Norouzinia
authors.affiliation: Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran.
authors.forename: Mostafa
authors.initials: M
authors.lastname: Hosseini
authors.affiliation: Proteomics Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
authors.forename: Aliasghar
authors.initials: A
authors.lastname: Keramatinia
authors.affiliation: Abadan School of Medical Sciences, Abadan, Iran.
authors.forename: Mostafa
authors.initials: M
authors.lastname: Jamalan
authors.affiliation: Hearing Disorders Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
authors.forename: Bijan
authors.initials: B
authors.lastname: Naghibzadeh
authors.affiliation: Department of Biomedical Engineering, Amirkabir University of Technology, Tehran, Iran.
authors.forename: Ali
authors.initials: A
authors.lastname: Sadeghi
authors.affiliation: Behbood Gastroenterology and Liver Diseases Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
authors.forename: Somayeh
authors.initials: S
authors.lastname: Jahani Sherafat
authors.affiliation: Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
authors.forename: Mohammad Reza
authors.initials: MR
authors.lastname: Zali
keywords: Hub-bottlenecks; Inflammatory bowel diseases (IBD); Protein clusters; Protein-protein interaction (PPI) network analysis