Protein-Protein Interaction Networks of Jasmonic Acid Synthesis in Arabidopsis thaliana and Gene Ontology Clustering
Abstract
Protein-protein interaction (PPI) networks can be reconstructed from public database and open-source bioinformatics tools. The aim of this work is to establish an PPI networks of homologous protein of jasmonic acid synthesis pathway in Arabidopsis thaliana from an existing co-expression network of van Verk et al. (2011) and compared them. We found that the extended PPI networks, comprising genetic and physical interactions, were different to the initial co-expression network, where the genes were linked by the expression patterns. However, the results of both biological interpretation on gene ontology are not different. Therefore, PPI network construction can not be applied to the case of jasmonic acid synthesis pathway. Gene ontology clustering was found to better contribute for biological interpretation. If the tools for gene ontology clustering and its database are developed in accordance with the purpose of the use, it will make biological interpretation more accurate and meet the demand. Keywords : protein-protein interaction networks, jasmonic acid synthesis, Arabidopsis thaliana, gene ontology clusteringReferences
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Lamesch, P., Berardini, T. Z., Li, D., Swarbreck, D., Wilks, C., Sasidharan, R., Muller, R., Dreher, K., Alexander, D. L., Garcia, H. M., Karthikeyan, A. S., Lee, C. H., Nelson, W. D., Ploetz, L., Singh, S., Wensel, A. and Huala, E. (2012). The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools. Nucleic Acids Res, 40, D1202 – D1210.
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Schaller, A. and Stintzi, A. (2009). Enzymes in jasmonate biosynthesis – Structure, function, regulation. Phytochemistry, 70, 1532 – 1538.
Shannon, P., Markiel, A., Ozier, O., Baliga, N. S., Wang, J. T., Ramage, D., Amin, N., Schwikowski, B. and Ideker, T. (2003). Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res, 13(11), 2498 – 2504.
Szklarczyk, D., Franceschini, A., Wyder, S., Forslund, K., Heller, D., Huerta-Cepas, J., Simonovic, M., Roth, A., Santos, A., Tsafou, K. P., Kuhn, M., Bork, P., Jensen, L. J. and von Mering, C. (2015). STRING v10: protein-protein interaction networks, integrated over the tree of life, Nucleic Acids Res, 43 (Database issue), D447 – D452.
Turner, J. G., Ellis, C. and Devoto, A. (2002). The jasmonate signal pathway. The Plant Cell, S153 – S164.
Umate, P. (2011). Genome-wide analysis of lipoxygenase gene family in Arabidopsis and rice. Plant Signaling & Behavior, 6(3), 335 – 338.
van Verk, M. C., Bol, J. F., Linthorst, H. J. M. (2011). Prospecting for genes involved in transcriptional regulation of plant defenses, a bioinformatics approach, BMC Plant Biology, 11, 88.
Wasternack, C. and Hause, B. (2013). Jasmonates: biosynthesis, perception, signal transduction and action in plant stress response, growth and development. An update to the 2007 review in Annals of Botany. Annal. of Botany, 111, 1021 – 1058.
Duangnapa, K. and Sootanan, P. (2015). Homologous protein interaction network and functional analysis of salicylic acid biosynthesis pathway. Proceeding of the 6th international conference on Computational Systems-Biology and Bioinformatics (CSBio2015), 59 – 63.
Finn, R. D., Bateman, A., Clements, J., Coggill, P., Eberhardt, R. Y., Eddy, S. R., Heger, A., Hetherington, K., Holm, L., Mistry, J., Sonnhammer, E. L. L., Tate, J. and Punta, M., (2014). The pfam protein families. Nucleic Acids Res, 40, D222 – D230.
Fitche, W. M. (1970). Distinguishing homologous from analogous proteins. Syst. Zool, 19(2), 99 – 113.
GO Consortium. (2017). Nucleic Acids Res.
Hall, T. A. (1999). BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symposium Series, 41, 95-98.
Jensen, S. A. (2001). Orthologs and paralogs - we need to get it right. Genome Biol, 2(8), 1002.1 – 1002.3.
Lamesch, P., Berardini, T. Z., Li, D., Swarbreck, D., Wilks, C., Sasidharan, R., Muller, R., Dreher, K., Alexander, D. L., Garcia, H. M., Karthikeyan, A. S., Lee, C. H., Nelson, W. D., Ploetz, L., Singh, S., Wensel, A. and Huala, E. (2012). The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools. Nucleic Acids Res, 40, D1202 – D1210.
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.
Pellegrini, M., Haynor, D. and Johnson, J. M. (2004). Protein interaction networks, Expert Rev. Proteomics, 1(2), 239 – 249.
Pieterse, C.M., Leon-Reyes, A., Van der Ent, S., Van Wees, S. C. (2009). Networking by small-molecule hormones in plant immunity. Nat. Chem. Biol, 5(5), 308 – 316.
Salwinski, L., Miller, C. S., Smith, A. J., Pettit, F. K., Bowie, J. U. and Eisenberg, D. (2004). The database of interacting proteins: 2004 update. Nucleic Acids Res, 32 (Database issue), D449 – D451.
Sayers, E. W., Barrett, T., Benson, D. A., Bolton, E., Bryant, S. H., Caneses, K., Chetvernin, V., Church, D. M., Dicuccio, M., Federgen, S., Feolo, M., Fingerman, I. M., Geer, L. Y., Helmberg, W., Kupustin, Y., Krasnov, S., Landsman, D., Lipman, D. J., Lu, Z., Madden, T. L., Magej, T., Maglott, D. R., Marchler, B. A., Miller, V., Karsch, M. l., Ostell, J., Panchenko, A., Phan, L., Pruitt, K. D., Schuler, G. D., Sequeira, E., Sherry, S. T., Shumway, M., Sirotkin, K., Slotta, D., Souvorov, A., Starchenko, G., Tatusova, T. A., Wagner, L., Wang, Y., Wilbur, W. J., Yaschenko, E. and Ye, J. (2012). Database resources of the national center for biotechnology information. Nucleic Acids Res, 40, D13 – D25.
Schaller, A. and Stintzi, A. (2009). Enzymes in jasmonate biosynthesis – Structure, function, regulation. Phytochemistry, 70, 1532 – 1538.
Shannon, P., Markiel, A., Ozier, O., Baliga, N. S., Wang, J. T., Ramage, D., Amin, N., Schwikowski, B. and Ideker, T. (2003). Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res, 13(11), 2498 – 2504.
Szklarczyk, D., Franceschini, A., Wyder, S., Forslund, K., Heller, D., Huerta-Cepas, J., Simonovic, M., Roth, A., Santos, A., Tsafou, K. P., Kuhn, M., Bork, P., Jensen, L. J. and von Mering, C. (2015). STRING v10: protein-protein interaction networks, integrated over the tree of life, Nucleic Acids Res, 43 (Database issue), D447 – D452.
Turner, J. G., Ellis, C. and Devoto, A. (2002). The jasmonate signal pathway. The Plant Cell, S153 – S164.
Umate, P. (2011). Genome-wide analysis of lipoxygenase gene family in Arabidopsis and rice. Plant Signaling & Behavior, 6(3), 335 – 338.
van Verk, M. C., Bol, J. F., Linthorst, H. J. M. (2011). Prospecting for genes involved in transcriptional regulation of plant defenses, a bioinformatics approach, BMC Plant Biology, 11, 88.
Wasternack, C. and Hause, B. (2013). Jasmonates: biosynthesis, perception, signal transduction and action in plant stress response, growth and development. An update to the 2007 review in Annals of Botany. Annal. of Botany, 111, 1021 – 1058.
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2019-01-10
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