Introduction of inflammatory bowel disease biomarkers panel using protein-protein interaction (PPI) network analysis
Gastroenterology and Hepatology from Bed to Bench,
Vol. 9 No. Supplement 1 (2016),
8 December 2016
https://doi.org/10.22037/ghfbb.v0i0.1046
Abstract
Aim: 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.
Conclusion: 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. Keywords: Inflammatory bowel diseases (IBD), Protein-protein interaction (PPI) network analysis, Hub-bottlenecks, Protein clusters
- Inflammatory bowel diseases (IBD)
- Protein-protein interaction (PPI) network analysis
- Hub-bottlenecks
- protein clusters
How to Cite
References
Bennike T, Birkelund S, Stensballe A, Andersen V. Biomarkers in inflammatory bowel diseases: current status and proteomics identification strategies. World J Gastroenterol. 2014;20(12):3231-44.
Burisch J, Jess T, Martinato M, Lakatos PL. The burden of inflammatory bowel disease in Europe. Journal of Crohn's and Colitis. 2013;7(4):322-37.
Molodecky NA, Soon S, Rabi DM, Ghali WA, Ferris M, Chernoff G, et al. Increasing incidence and prevalence of the inflammatory bowel diseases with time, based on systematic review. Gastroenterology. 2012;142(1):46-54. e42.
Loftus EV. Clinical epidemiology of inflammatory bowel disease: incidence, prevalence, and environmental influences. Gastroenterology. 2004;126(6):1504-17.
Ng SC, Leung WK, Shi HY, Li MK, Leung CM, Ng CK, et al. Epidemiology of Inflammatory Bowel Disease from 1981 to 2014: Results from a Territory-Wide Population-Based Registry in Hong Kong. Inflammatory Bowel Diseases. 2016;22(8):1954-60.
Amre DK, D'souza S, Morgan K, Seidman G, Lambrette P, Grimard G, et al. Imbalances in dietary consumption of fatty acids, vegetables, and fruits are associated with risk for Crohn's disease in children. The American journal of gastroenterology. 2007;102(9):2016-25.
Jantchou P, Morois S, Clavel-Chapelon F, Boutron-Ruault M-C, Carbonnel F. Animal protein intake and risk of inflammatory bowel disease: The E3N prospective study. The American journal of gastroenterology. 2010;105(10):2195-201.
Xavier R, Podolsky D. Unravelling the pathogenesis of inflammatory bowel disease. Nature. 2007;448(7152):427-34.
Khor B, Gardet A, Xavier RJ. Genetics and pathogenesis of inflammatory bowel disease. Nature. 2011;474(7351):307-17.
Henderson P, Anderson NH, Wilson DC. The diagnostic accuracy of fecal calprotectin during the investigation of suspected pediatric inflammatory bowel disease: a systematic review and meta-analysis. The American journal of gastroenterology. 2014;109(5):637-45.
Lewis JD. The utility of biomarkers in the diagnosis and therapy of inflammatory bowel disease. Gastroenterology. 2011;140(6):1817-26. e2.
Mansouri V, Vafaee R, Abaszadeh H, Heidari M. Protein-protein interaction network analysis of obesity. Arvand Journal of Health and Medical Sciences. 2016;1(3).
Safari‐Alighiarloo N, Taghizadeh M, Tabatabaei SM, Shahsavari S, Namaki S, Khodakarim S, et al. Identification of new key genes for type 1 diabetes through construction and analysis of the protein‐protein interaction networks based on blood and pancreatic islet transcriptomes. Journal of Diabetes. 2016.
Azodi MZ, Peyvandi H, Nejad MR, Safaei A, Rostami K, Vafaee R, et al. Protein-Protein Interaction Network of Celiac Disease. Gastroenterology and Hepatology from bed to bench. 2016.
Safaei A, Tavirani MR, Oskouei AA, Azodi MZ, Mohebbi SR, Nikzamir AR. Protein-protein interaction network analysis of cirrhosis liver disease. Gastroenterology and Hepatology from bed to bench. 2016;9(2):114.
Zamanian-Azodi M, Mortazavi-Tabatabaei SA, Mansouri V, Vafaee R. Metabolite-protein interaction (MPI) network analysis of obsessive-compulsive disorder (OCD) from reported metabolites. Arvand Journal of Health and Medical Sciences. 2016.
Bader GD, Hogue CW. An automated method for finding molecular complexes in large protein interaction networks. BMC bioinformatics. 2003;4(1):1.
Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome research. 2003;13(11):2498-504.
Szklarczyk D, Morris JH, Cook H, Kuhn M, Wyder S, Simonovic M, et al. The STRING database in 2017: quality-controlled protein–protein association networks, made broadly accessible. Nucleic Acids Research. 2016:gkw937.
Meuwis M-A, Fillet M, Geurts P, De Seny D, Lutteri L, Chapelle J-P, et al. Biomarker discovery for inflammatory bowel disease, using proteomic serum profiling. Biochemical pharmacology. 2007;73(9):1422-33.
Li X, Conklin L, Alex P. New serological biomarkers of inflammatory bowel disease. World journal of gastroenterology: WJG. 2008;14(33):5115.
Jafari M, Sadeghi M, Mirzaie M, Marashi S-A, Rezaei-Tavirani M. Evolutionarily conserved motifs and modules in mitochondrial protein–protein interaction networks. Mitochondrion. 2013;13(6):668-75.
Zamanian-Azodi M, Rezaei-Tavirani M, Rahmati-Rad S, Hasanzadeh H, Tavirani MR, Seyyedi SS. Protein-Protein Interaction Network could reveal the relationship between the breast and colon cancer. Gastroenterology and Hepatology from bed to bench. 2015;8(3):215.
Li Y, de Haar C, Peppelenbosch MP, van der Woude CJ. New insights into the role of STAT3 in IBD. Inflammatory bowel diseases. 2012;18(6):1177-83.
- Abstract Viewed: 559 times
- PDF Downloaded: 162 times