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.