Bioinformatics analysis of defense associated transcriptional networks

Our study here in Bioinformatics pivots around GeneChip technology-coupled with parallel expression analysis. In collaboration with Syngenta we utilize expression analysis to identify gene activity patterns associated with plant immune responses to pathogenic microorganisms such as Peronospera Parasitica and Pseudomonas Syringae. This study, performed by many scientists in the lab, helps to achieve a more global understanding of genetic function and regulation in the field of plant pathology. Currently in use is a custom Arabidopsis thaliana whole genome array that contains 26412 probe sets representing 26367 Arabidopsis genes. Previously (before 2002), another custom chip was used that contained ~ 8600 probe sets. This chip contained roughly 32 probes per gene and covered around 1/3rd of the genome.

Analysis of gene activity patters is performed with multiple graphics display programs such as those found in the Michael Eisen's Software package (Cluster and TreeView) and in Silicon Genetics' GeneSpring. Cluster and TreeView provides a quick, yet distinctive method for the generation of well-defined gene clusters based on common expression characteristics. GeneSpring is a more comprehensive tool used for displaying anything from expression profiling to physical positioning and statistical selection. Current examples of such analysis can be seen in other lab publications.
Some of the ultimate goals are to discover genes that are activated specifically in response to certain defense treatments and to assign these to defined pathways of the plant immune system. In addition, we categorize genes based on their responses to a variety of different defense-related treatments. In promoters of strictly co-regulated genes we identified (with the help of AlignACE and BioProspector) highly conserved sequence motifs, which may be binding sites of transcription factors responsible for their co-regulation

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