Fig. 4

lncRNA expression for four modules associated with heat stress. This figure consists of a heat map (top) and graphs of the expression of specific TE-lncRNAs (bottom) that were chosen because they were top three overrepresented lncRNAs in the four modules and had high interconnectivity. Top) The heat graph shows transcript expression levels for hub genes and lncRNAs in each module (y-axis) and across conditions (x-axis). The key to modules (y-axis) and stress conditions (x-axis) are shown on the right legend, with conditions also separated by developmental stage (bottom of x-axis). Warmer colors within the heat map indicate high expression, and cooler colors are low (or under) expression. This particular heat map illustrates that the four heat-associated modules are, as expected, highly expressed under heat stress, but not always at the same developmental stage. Bottom) The bar plots below the heat graph are eigen-lncRNA expression values selected from the top three overrepresented TE-lncRNAs with high interconnectivity. The x-axis is the same as the heat map, and the id of the TE-lncRNAs is provided by the color key. This graphs shows, again, that the TE-lncRNAs tend to be more highly expressed under heat stress, but with some dependence on developmental stage. Additional file 1: Figs. S5 to S9 present similar figures for modules associated with cold, drought, salt, UV and ozone stress, respectively