Expression patterns and fold changes of differentially-expressed genes. Differentially-expressed genes in panicle, leaf, and root, among 93-11 (N), PA64s (P), and their F1 hybrid LYP9 (L) are shown. Twelve different patterns were labeled in each slice and their graphical indicators were displayed surrounding the three panels. The radius at which a gene is plotted represents log2 of the fold change between the high and low values among three rice cultivars, and the angle represents the relationships between LYP9 and its parents. Differential expressed genes with significance intervals of 0.01 <P < 0.05 and P < 0.01 are shown in blue and green, respectively. Only tags that exhibited changes of <16-fold are plotted since those beyond the fold value are very limited in numbers (listed in Additional file 5). Note (1) genes harbored by the five patterns above the horizontal lines in each panel are up-regulated (positive heterosis) in hybrid, (2) genes in the five patterns in each panel below the horizontal lines are down-regulated (negative heterosis) in hybrid, and (3) two mid-parent patterns are on the horizontal lines.