Module 9 generated based on overlapped DEGs. The tree-like upper part visualizes the predicted regulatory decision tree of the module, where a tree node (i.e. color bar) represents a query on the expression level of a predicted TF and a branch (i.e. arrowed edge) denotes a yes / no answer (highly / lowly expressed or not) to the query. The family names and gene IDs of the predicted TFs are listed above the nodes. A path from the top to a sub-set of conditions shown in the square box at the bottom predicts that the TFs on the path collaboratively regulate the expression of the genes in these conditions. For example, the right most path suggests that, if Homeodomain is highly expressed, Nin-like highly expressed, and GRAS highly expressed, the genes in the modules will be regulated in the nodulation conditions (i.e., conditions 34 and 3). The colored square box visualizes the expression levels of all genes in the module across all the conditions, where a row denotes a gene and a column denotes an experimental condition. The color bar on the right illustrates a specific color with an expression value, from the lowest (green) to the highest (red). The numbers at the bottom of the figure corresponds to the experimental conditions, which are described in details in the Additional file 1.