title: Pathway reconstruction of airway remodeling in chronic lung diseases: a systems biology approach.
abstract: Airway remodeling is a pathophysiologic process at the clinical, cellular, and molecular level relating to chronic obstructive airway diseases such as chronic obstructive pulmonary disease (COPD), asthma and mustard lung. These diseases are associated with the dysregulation of multiple molecular pathways in the airway cells. Little progress has so far been made in discovering the molecular causes of complex disease in a holistic systems manner. Therefore, pathway and network reconstruction is an essential part of a systems biology approach to solve this challenging problem. In this paper, multiple data sources were used to construct the molecular process of airway remodeling pathway in mustard lung as a model of airway disease. We first compiled a master list of genes that change with airway remodeling in the mustard lung disease and then reconstructed the pathway by generating and merging the protein-protein interaction and the gene regulatory networks. Experimental observations and literature mining were used to identify and validate the master list. The outcome of this paper can provide valuable information about closely related chronic obstructive airway diseases which are of great importance for biologists and their future research. Reconstructing the airway remodeling interactome provides a starting point and reference for the future experimental study of mustard lung, and further analysis and development of these maps will be critical to understanding airway diseases in patients.
authors: Laboratory of Systems Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran.
authors: Ali
authors: A
authors: Najafi
authors: Laboratory of Systems Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran.
authors: Ali
authors: A
authors: Masoudi-Nejad
authors: Genomics Division, Chemical Injury Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran.
authors: Mostafa
authors: M
authors: Ghanei
authors: Genomics Division, Chemical Injury Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran.
authors: Mohamad-Reza
authors: MR
authors: Nourani
authors: Laboratory of Systems Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran; Department of Algorithms and Computation, College of Engineering, University of Tehran, Tehran, Iran.
authors: Ali
authors: A
authors: Moeini
mesh_terms: D056151:Airway Remodeling / Q000235:genetics*; D001249:Asthma / Q000235:genetics / Q000378:metabolism* / Q000473:pathology; D002908:Chronic Disease; D057225:Data Mining; D030541:Databases, Genetic; D053263:Gene Regulatory Networks; D006801:Humans; D008168:Lung / Q000378:metabolism* / Q000473:pathology; D009151:Mustard Gas; D025941:Protein Interaction Mapping; D029424:Pulmonary Disease, Chronic Obstructive / Q000139:chemically induced / Q000235:genetics / Q000378:metabolism* / Q000473:pathology; D049490:Systems Biology
chemical_list: D009151:Mustard Gas