Exploring Anti-Inflammatory Mechanisms of Onion Bioactive Compounds with Module-Based Protein Interaction Network Analysis
Abstract
Onion (Allium cepa L.) is a popular plant used as an ingredient in many dishes. This plant is a rich source of several natural active compounds, especially, flavonoids are enriched in onion and has pharmacological effects on the anti-inflammation. Biological network and module-base analysis can be employed to find a role and molecular mechanisms involving the anti-inflammation of flavonoid in onion. In this study, we aimed to use bioinformatic tools to search for potential target proteins, protein-protein interactions, and the proteins involving anti-inflammatory pathways. The module-based network analysis and biological interpretation were performed. From the analyses, we have found five active compounds in onions, relating to the MAPK and NF-References
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Li, M., Wang, J. and Chen, J. E. (2008). A Fast Agglomerate Algorithm for Mining Functional Modules in Protein Interaction Networks. BioMedical Engineering and Informatics, 121(2008), 3-7.
Liang, Y. C., Huang, Y. T., Tsai, S. H., Lin-Shiau, S. Y., Chen, C. F. and Lin, J. K. (1999). Suppression of inducible cyclooxygenase and inducible nitric oxide synthase by apigenin and related flavonoids in mouse macrophages. Carcinogenesis, 20(10), 1945-1952.
Maere, S., Heymans, K. and Kuiper, M. (2005). BiNGO: a Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks. Bioinformatics, 21(16), 3448-3449.
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Morrison, D. K. (2012). MAP kinase pathways. Cold Spring Harbor Perspectives in Biology, 4(11), a011254.
Nair, M. P., Mahajan, S., Reynolds, J. L., Aalinkeel, R., Nair, H., Schwartz, S. A. and Kandaswami, C. (2006). The flavonoid quercetin inhibits proinflammatory cytokine (tumor necrosis factor alpha) gene expression in normal peripheral blood mononuclear cells via modulation of the NF-
Bader, G. D. and Hogue C. W. (2003). An automated method for finding molecular complexes in large protein interaction networks. BMC Bioinformatics, 4, 2.
Bindea, G., Mlecnik, B., Hackl, H., Charoentong, P., Tosolini, M., Kirilovsky, A., Fridman, W. H., Pagès, F. and Galon, J. (2009). ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks. Bioinformatics, 25(8), 1091-1093.
Davies, M., Nowotka, M., Papadatos, G., Dedman, N., Gaulton, A., Atkinson, F., Bellis, L. and Overington, J. P. (2015). ChEMBL web services: streamlining access to drug discovery data and utilities. Nucleic Acids Research, 43, W612–W620.
Forlim, C. G., Haghiri, S., Düzel, S. and Kühn, S. (2019). Efficient small-world and scale-free functional brain networks at rest using k-nearest neighbors thresholding. Biorxiv, 628453.
Gan, Y., Zheng, S., Baak, J.P., Zhao, S., Zheng, Y., Luo, N., Liao, W. and Fu, C. (2015). Prediction of the anti-inflammatory mechanisms of curcumin by module-based protein interaction network analysis. Acta Pharmaceutica Sinica B, 5(6), 590-595.
Garcia, O., Saveanu, C., Cline, M., Fromont-Racine, M., Jacquier, A., Schwikowski, B. and Aittokallio, T. (2006). GOlorize: a Cytoscape plug-in for network visualization with Gene Ontology-based layout and coloring. Bioinformatics, 23(3), 394-396.
Gebretsadik, K. and Dechassa, N. (2018). Response of Onion (Allium cepa L.) to nitrogen fertilizer rates and spacing under rain fed condition at Tahtay Koraro, Ethiopia. Scientific Reports, 8(1), 1-8.
Huang, D. W., Sherman, B. T., & Lempicki, R. A. (2009). Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nature Protocols, 4(1), 44.
Kim, J. H., Kim, M. Y., Kim, J. H. and Cho, J. Y. (2015). Fisetin suppresses macrophage-mediated inflammatory responses by blockade of Src and Syk. Biomolecules & Therapeutics, 23(5), 414.
Kim, S. H., Park, J. G., Lee, J., Yang, W. S., Park, G. W., Kim, H. G., Yi, Y. S., Baek, K. S., Sung, N. Y., Hossen, M. J., Lee, M. N., Kim, J. H. and Cho, J. Y. (2015). The dietary flavonoid Kaempferol mediates anti-inflammatory responses via the Src, Syk, IRAK1, and IRAK4 molecular targets. Mediators of Inflammation, 2015, 1-15.
Kim, S. J., Ko, W. K., Jo, M. J., Arai, Y., Choi, H., Kumar, H., Han, I. B. and Sohn, S. (2018). Anti-inflammatory effect of tauroursodeoxycholic acid in RAW 264.7 macrophages, bone marrow-derived macrophages, BV2 microglial cells, and spinal cord injury. Scientific Reports, 8(1), 3176.
King, A. D., Pržulj, N. and Jurisica, I. (2004). Protein complex prediction via cost-based clustering. Bioinformatics, 20(17), 3013-3020.
Kwak, J. H., Seo, J. M., Kim, N. H., Arasu, M. V., Kim, S., Yoon, M. K. and Kim, S. J. (2017). Variation of quercetin glycoside derivatives in three onion (Allium cepa L.) varieties. Saudi Journal of Biological Sciences, 24(6), 1387-1391.
Lee, H. N., Shin, S. A., Choo, G. S., Kim, H. J., Park, Y. S., Kim, B. S., Kim, S. K., Cho, S. D., Nam, J. S., Choi, C. S., Che, J. H., Park, B. K. and Jung, J. Y. (2018). Anti-inflammatory effect of quercetin and galangin in LPS-stimulated RAW264. 7 macrophages and DNCB-induced atopic dermatitis animal models. International Journal of Molecular Medicine, 41(2), 888-898.
Li, M., Wang, J. and Chen, J. E. (2008). A Fast Agglomerate Algorithm for Mining Functional Modules in Protein Interaction Networks. BioMedical Engineering and Informatics, 121(2008), 3-7.
Liang, Y. C., Huang, Y. T., Tsai, S. H., Lin-Shiau, S. Y., Chen, C. F. and Lin, J. K. (1999). Suppression of inducible cyclooxygenase and inducible nitric oxide synthase by apigenin and related flavonoids in mouse macrophages. Carcinogenesis, 20(10), 1945-1952.
Maere, S., Heymans, K. and Kuiper, M. (2005). BiNGO: a Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks. Bioinformatics, 21(16), 3448-3449.
McKusick, V. A. (2007). Mendelian Inheritance in Man and its online version, OMIM. The American Journal of Human Genetics, 80(4), 588-604.
Morrison, D. K. (2012). MAP kinase pathways. Cold Spring Harbor Perspectives in Biology, 4(11), a011254.
Nair, M. P., Mahajan, S., Reynolds, J. L., Aalinkeel, R., Nair, H., Schwartz, S. A. and Kandaswami, C. (2006). The flavonoid quercetin inhibits proinflammatory cytokine (tumor necrosis factor alpha) gene expression in normal peripheral blood mononuclear cells via modulation of the NF-
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2020-05-01
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