Differences in gene expression in the first 12 hours after virus inoculation were investigated in two differently sensitive potato cultivars. In both cultivars, genes involved in photosynthesis were upregulated at 30 minutes and downregulated 12 hours following virus inoculation. Genes that responded differently in the two cultivars were involved in cell wall, plant hormones and secondary metabolite metabolism, signalling and defence. The results were published in one of the top journals in the field of plant science.
COBISS.SI-ID: 1940815
In collaboration with the authors of MapMan, an omics data visualization tool, originally developed for Arabidopsis, we have adapted the tool to allow visualization of potato TIGR 10k gene expression data. Special emphasis was given to the visualization of the expression of genes involved in the biotic stress response. In this way, biological interpretation of potato gene expression data was improved.
COBISS.SI-ID: 23317465
With a goal to increase robustness of microarray data we have studied the effect of different preprocessing methods (background correction, normalization, dealing with duplicate spots) on final results of statistical analysis. Since the effect was found to be significant, we have proposed a data analysis workflow where preprocessing methods are selected on the basis of data type and quality and an intersection of results obtained by two different preprocessing methods is used as a final differentially expressed gene list.
COBISS.SI-ID: 1888847
Microarray analysis enables identification of genes, proteins and signal molecules involved in plant response to pathogen infection. In a chapter in the book Plant Virology Protocols we have published protocols for sample preparation, »potato TIGR 10k arrays« microarray hybridization and data analysis. All protocols were developed at our Department. The book rates as second most sold in the field of plant molecular biology on web store Amazon.com.
COBISS.SI-ID: 1859407