The majority of these genes (261 genes) was up-regulated, whereas only 41 genes were down-regulated
(Figure 3). Although most of the regulated genes have been functionally annotated, a significant proportion (~23%) remained of unknown function, among which 19 genes were unique for FZB42. In addition, 44 genes (~15%) encoded either hypothetical proteins or proteins with putative functions (Figure 3). The distribution in various functional categories of all the gene with known (189 genes) or putative (44 genes) products are summarized in Figure 4. Figure 3 Overview of groups of the 302 genes altered in transcription by root exudates. BAY 80-6946 price A total of 302 genes were significantly altered (q ≤ 0.01 and fold change ≥1.5) in transcription by the maize root exudates. “Up” indicates genes that were up-regulated in presence root exudates, while “down” the ones that were down-regulated by the root exudates. The genes encoding a product with known or unknown function and those encoding a hypothetical protein were indicated. The number of genes of each section and their percentage is depicted. Figure 4 Distribution in various functional categories of the genes altered in transcription by root exudates. Among the 302 genes altered in transcription by maize root BAY 11-7082 cost exudates at OD3.0,
those with known (189 genes) or putative (44 genes) products were classified according to their function. The percentage of each group is indicated. Validation of microarray result by real-time PCR Nine up-regulated genes with different levels of fold changes in expression (1.5 ~ 5.2 fold) were OTX015 nmr chosen to be evaluated by quantitative real-time PCR. All these genes were confirmed to be significantly Farnesyltransferase up-regulated in the presence of root exudates (Figure 5). The fold change of each gene revealed by
real-time PCR was similar to that obtained in the microarray experiments (Figure 5). In summary, the real-time PCR suggested that the microarray data were reliable. Figure 5 Fold-change of differentially expressed genes selected for validation by Real-time PCR. The fold changes revealed by real-time PCR of the selected genes were determined using the software REST. Three repeats were performed for each gene. For comparison, the fold changes obtained in microarray analysis were shown in parenthesis below each specific gene. The boxes represent the distance between the 25th and the 75th percentile. The lines in the boxes represent the median gene expression. Whiskers represent the minimum and maximum observations. The regulated genes with known function Among the 302 genes with significantly altered expression by root exudates, 189 were annotated with known functions. These were categorized into various classes , such as cell envelope and cellular processes, intermediary metabolism, information pathway and other functions .