Figure 4

Genome distribution of the genes with altered expression levels in DpDf plants. Using a bioinformatic approach, we were able to infer the map positions for ~7,000 microarray probe sets. The probe sets were divided into the 10 separate plots (one for each maize chromosome). The log₂ of the average DpDf microarray signal divided by the average wild-type microarray signal is plotted on the y-axis and the cM (based on IBM 2004 coordinates) is plotted along the x-axis. A log₂ value of 0 corresponds to equal expression levels in DpDf and wild type. A log₂ value of 1.0 indicates two-fold higher expression in DpDf than in wild-type while a log₂ value of -1.0 indicates two-fold lower expression in DpDf than in wild-type. The blue triangles indicate genes that were found to have statistically significant differential expression in DpDf and wild-type plants (and passed the minimum signal and fold-change filters). The red squares indicate genes that were not deemed to have statistically significant differential expression. The regions of chromosome 5 and 6 that are present in altered copy number are indicated by black bars.