title: Network analysis and cross species comparison of protein-protein interaction networks of human, mouse and rat cytochrome P450 proteins that degrade xenobiotics.
abstract: Cytochrome P450 (CYP) enzymes that degrade xenobiotics play a critical role in the metabolism and biotransformation of drugs and xenobiotics in humans as well as experimental animal models such as mouse and rat. These proteins function as a network collectively as well as independently. Though there are several reports on the organization, regulation and functionality of various CYP enzymes at the molecular level, the understanding of organization and functionality of these proteins at the holistic level remain unclear. The objective of this study is to understand the organization and functionality of xenobiotic degrading CYP enzymes of human, mouse and rat using network theory approaches and to study species differences that exist among them at the holistic level. For our analysis, a protein-protein interaction (PPI) network for CYP enzymes of human, mouse and rat was constructed using the STRING database. Topology, centrality, modularity and robustness analyses were performed for our predicted CYP PPI networks that were then validated by comparison with randomly generated network models. Network centrality analyses of CYP PPI networks reveal the central/hub proteins in the network. Modular analysis of the CYP PPI networks of human, mouse and rat resulted in functional clusters. These clusters were subjected to ontology and pathway enrichment analysis. The analyses show that the cluster of the human CYP PPI network is enriched with pathways principally related to xenobiotic/drug metabolism. Endo-xenobiotic crosstalk dominated in mouse and rat CYP PPI networks, and they were highly enriched with endogenous metabolic and signaling pathways. Thus, cross-species comparisons and analyses of human, mouse and rat CYP PPI networks gave insights about species differences that existed at the holistic level. More investigations from both reductionist and holistic perspectives can help understand CYP metabolism and species extrapolation in a much better way.
authors.affiliation: Department of Bioinformatics, School of Life Sciences, Bharathidasan University, Tiruchirappalli 620 024, Tamil Nadu, India. bdupartha@gmail.com partha@bdu.ac.in and Mahatma Gandhi-Doerenkamp Center (MGDC) for Alternatives to Use of Animals in Life Science Education, Bharathidasan University, Tiruchirappalli 620 024, Tamil Nadu, India. mgdcaua@yahoo.in akbarbdu@gmail.com.
authors.forename: Bagavathy Shanmugam
authors.initials: BS
authors.lastname: Karthikeyan
authors.affiliation: Mahatma Gandhi-Doerenkamp Center (MGDC) for Alternatives to Use of Animals in Life Science Education, Bharathidasan University, Tiruchirappalli 620 024, Tamil Nadu, India. mgdcaua@yahoo.in akbarbdu@gmail.com.
authors.forename: Mohammad Abdulkader
authors.initials: MA
authors.lastname: Akbarsha
authors.affiliation: Department of Bioinformatics, School of Life Sciences, Bharathidasan University, Tiruchirappalli 620 024, Tamil Nadu, India. bdupartha@gmail.com partha@bdu.ac.in.
authors.forename: Subbiah
authors.initials: S
authors.lastname: Parthasarathy
mesh_terms: D000818:Animals; D001711:Biotransformation; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods; D003577:Cytochrome P-450 Enzyme System / Q000378:metabolism*; D030562:Databases, Protein; D006801:Humans; D007527:Isoenzymes; D051379:Mice; D025941:Protein Interaction Mapping / Q000379:methods; D060066:Protein Interaction Maps; D051381:Rats; D015203:Reproducibility of Results; D015262:Xenobiotics / Q000378:metabolism*
chemical_list: D007527:Isoenzymes; D015262:Xenobiotics; D003577:Cytochrome P-450 Enzyme System