title: A Systems Biology Methodology Combining Transcriptome and Interactome Datasets to Assess the Implications of Cytokinin Signaling for Plant Immune Networks.
abstract: Cytokinins (CKs) play an important role in plant growth and development. Also, several studies highlight the modulatory implications of CKs for plant-pathogen interaction. However, the underlying mechanisms of CK mediating immune networks in plants are still not fully understood. A detailed analysis of high-throughput transcriptome (RNA-Seq and microarrays) datasets under modulated conditions of plant CKs and its mergence with cellular interactome (large-scale protein-protein interaction data) has the potential to unlock the contribution of CKs to plant defense. Here, we specifically describe a detailed systems biology methodology pertinent to the acquisition and analysis of various omics datasets that delineate the role of plant CKs in impacting immune pathways in Arabidopsis.
authors.affiliation: Functional Genomics & Systems Biology Group, Department of Bioinformatics, Biocenter, University of Wuerzburg, 97074, Wuerzburg, Germany.
authors.forename: Meik
authors.initials: M
authors.lastname: Kunz
authors.affiliation: Deptartment of Bioinformatics, Biocenter University of Würzburg Am Hubland Würzburg Germany, Julius-Maximilians-Universität Würzburg, Würzburg, Germany.
authors.forename: Thomas
authors.initials: T
authors.lastname: Dandekar
authors.affiliation: Deptartment of Bioinformatics, Biocenter University of Würzburg Am Hubland Würzburg Germany, Julius-Maximilians-Universität Würzburg, Würzburg, Germany. muhammad@biozentrum.uni-wuerzburg.de.|Department of Molecular Biology and Genetics, Boğaziçi University, North Campus Kuzey Park Building 310, 34342, Bebek, Istanbul, Turkey. muhammad@biozentrum.uni-wuerzburg.de.
authors.forename: Muhammad
authors.initials: M
authors.lastname: Naseem
mesh_terms: D017360:Arabidopsis / Q000235:genetics / Q000276:immunology / Q000378:metabolism; D019295:Computational Biology / Q000379:methods; D003583:Cytokinins / Q000378:metabolism*; D030541:Databases, Genetic; D018506:Gene Expression Regulation, Plant; D057865:Plant Immunity; D015398:Signal Transduction; D012984:Software; D049490:Systems Biology / Q000379:methods; D059467:Transcriptome
chemical_list: D003583:Cytokinins
keywords: Cytokinins; Interactomes; Plant hormones; Plant immunity; Transcriptomes