title: Construction and analysis of the protein-protein interaction networks based on gene expression profiles of Parkinson's disease.
abstract: BACKGROUND
  Parkinson's Disease (PD) is one of the most prevailing neurodegenerative diseases. Improving diagnoses and treatments of this disease is essential, as currently there exists no cure for this disease. Microarray and proteomics data have revealed abnormal expression of several genes and proteins responsible for PD. Nevertheless, few studies have been reported involving PD-specific protein-protein interactions.
  
  
  RESULTS
  Microarray based gene expression data and protein-protein interaction (PPI) databases were combined to construct the PPI networks of differentially expressed (DE) genes in post mortem brain tissue samples of patients with Parkinson's disease. Samples were collected from the substantia nigra and the frontal cerebral cortex. From the microarray data, two sets of DE genes were selected by 2-tailed t-tests and Significance Analysis of Microarrays (SAM), run separately to construct two Query-Query PPI (QQPPI) networks. Several topological properties of these networks were studied. Nodes with High Connectivity (hubs) and High Betweenness Low Connectivity (bottlenecks) were identified to be the most significant nodes of the networks. Three and four-cliques were identified in the QQPPI networks. These cliques contain most of the topologically significant nodes of the networks which form core functional modules consisting of tightly knitted sub-networks. Hitherto unreported 37 PD disease markers were identified based on their topological significance in the networks. Of these 37 markers, eight were significantly involved in the core functional modules and showed significant change in co-expression levels. Four (ARRB2, STX1A, TFRC and MARCKS) out of the 37 markers were found to be associated with several neurotransmitters including dopamine.
  
  
  CONCLUSIONS
  This study represents a novel investigation of the PPI networks for PD, a complex disease. 37 proteins identified in our study can be considered as PD network biomarkers. These network biomarkers may provide as potential therapeutic targets for PD applications development.
authors.affiliation: Integrated Science Education & Research Centre (ISERC), Visva-Bharati University, Shantiniketan, Birbhum, West Bengal, India.
authors.forename: Hindol
authors.initials: H
authors.lastname: Rakshit
authors.affiliation: Cognizant Technology Solutions India Pvt. Ltd., Rajiv Gandhi Infotech Park, MIDC, Hinjewadi, Pune, Maharashtra, India.
authors.forename: Nitin
authors.initials: N
authors.lastname: Rathi
authors.affiliation: Department of Biophysics, Bose Institute, Acharya J.C. Bose Centenary Building, Kolkata, West Bengal, India.
authors.forename: Debjani
authors.initials: D
authors.lastname: Roy
mesh_terms: D001921:Brain / Q000378:metabolism / Q000473:pathology*; D020869:Gene Expression Profiling; D006801:Humans; D010300:Parkinson Disease / Q000235:genetics / Q000378:metabolism*; D025941:Protein Interaction Mapping; D060066:Protein Interaction Maps; D011506:Proteins / Q000235:genetics / Q000378:metabolism*; D040901:Proteomics; D013378:Substantia Nigra / Q000378:metabolism / Q000473:pathology; D059467:Transcriptome
chemical_list: D011506:Proteins