Abstract
The study and systematic analysis of protein–protein interaction networks relevant to disease or well-being have become an integral part of systems biology. Recent studies have revealed strong association between the topological properties and biological function of proteins in networks. Hypoxia is a pathophysiological condition which arises due to low oxygen concentration in conditions like prenatal birth, cardiovascular diseases, malignancies, inflammation, ascent to higher altitude, free diving, etc. Conventional techniques of studying a single gene or protein have not been successful in this complex disorder. Considering the complexity and multivariate nature of hypoxic stress, we aimed to identify the key proteins; the central biological regulatory pathways, and their molecular connectivity by the topological analysis of the protein–protein interaction (PPI) network. The study collected proteins whose expressions are altered in response to hypoxia, and calculated an interaction map which is termed as the giant core “hypoxia-responsive PPI network” of 603 nodes connected via 4264 edges. A backbone network of 24 bottleneck proteins with high Betweenness Centrality and large degree was identified. The robustness and accuracy of backbone network was validated by 104 test networks. The giant network was divided into five functional subnetworks, each enriched with important and distinct biological pathways. The study is the first methodological network and pathway enrichment analysis of hypoxia-regulated proteins which sheds light on the important molecular mechanisms operational during hypoxic stress. It also comprehensively describes the global protein–protein interactions, the biological subnetworks, and the backbone network regulating the hypoxic stress response. This helps to identify potential target molecules for therapy or ameliorating the pathophysiology, which could not be found merely through molecular biology methods. In principle, the methodology described may be implemented to understand the molecular mechanisms in other multivariate disorders.
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The authors are thankful to Ms. Mitali Kaushik, Jamia Milia Islamia for the help in the preparation of figures.
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Khurana, P., Tiwari, D., Sugadev, R. et al. A comprehensive assessment of networks and pathways of hypoxia-associated proteins and identification of responsive protein modules. Netw Model Anal Health Inform Bioinforma 5, 17 (2016). https://doi.org/10.1007/s13721-016-0123-8
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DOI: https://doi.org/10.1007/s13721-016-0123-8