Towards a temporal modeling of the genetic network controlling Systemic Acquired Resistance in Arabidopsis thaliana

Abstract

Abstract-We studied defense mechanism of the Arabidopsis thaliana subjected to Salicylic Acid (SA) treatment for 0, 1, and 8 hours using a broader application of the frequent itemset approach. Four genotypes of the plant were used in this study, Columbia wild type, mutant npr1, double mutant tga1 ga4 and triple mutant tga2 ga5 ga6. We defined the major patterns of transcription regulation governing pathogen defense mechanism, thereby creating a model of the Systemic Acquired Resistance (SAR) at three time points. The temporal model describes the relationships among the regulators and defines groups of genes that are subject to similar regulation. The results obtained offered a first glimpse into the temporal pattern of the gene network controlling SAR in plant. We found that most of the genes that responded to SA challenge are in fact dependent on one or more of the NPR1 and TGA transcription factors tested in this study.

GOAL: A software tool for assessing biological significance of genes groups

“…The data used for these analyses are provides in the GOAL tool as default data and can be exploited by the users in their own research. GOAL has also been successfully used to characterize the following six human genes (IFNA4 IL12B IL2RB STAT1 STAT2 IRF9) provided to us by one of the reviewers (Additional File 3 ), to characterize groups of correlated genes in DNA microarray experimental data of Arabidopsis thaliana under pathogens attack [ 44 ], and several in house (private) DNA microarray datasets of Brassica napus during seed development.…”

Integrative Data Mining in Functional Genomics of Brassica napus and Arabidopsis thaliana

“…In the second phase, SA was applied to all four genotypes. The knowledge discovery was done by using integration of an expanded version of frequent itemset mining approach [18] and an order preserving three-dimensional-clustering approach [19]. The order preserving clustering approach is a combination of order preserving pattern feature [20] with clustering.…”

“…Before applying the expanded version of frequent itemset mining algorithm, the gene expression matrix was first discretized into three distinct values (-1, 0, 1) representing down-regulation, no significant difference, and up-regulation, respectively, based on a predefined threshold value, and relative to a baseline, which is the wild type in our study. All the interesting associations and association rules between the transcription factors and their target genes were then identified [18]. A wiring diagram was inferred to describe gene regulatory network during pathogen-induced SAR in A. thaliana specifying sets of genes that were differentially expressed as a result of one, two or all three mutant sets (npr1, tga1 tga4, and tga2 tga5 tga6) (Fig.…”

“…In the second phase, through the frequent itemset mining approach [18], we were able to identify genes that were regulated by one set of transcription factors alone, and those collectively regulated by two or all three sets of transcription factors. For example, the wiring diagram in Fig.…”