Fig. 2

The flow diagram for revealing the critical transition state. a With samples in previous and the current time points designated as the control and case sample respectively. The 14 different developmental stages from initial to mature were divided into 13 combinations. b We applied DNB method to reveal a critical differentiation state of Arabidopsis flower development by comparing the control and case samples. c To construct the gene regulatory network controlling the flowering transition, we applied NARROMI algorithm on the expression data of the transition-specific genes. The NARROMI algorithm removes noisy regulations with low pair-wise correlations and redundant regulations from indirect regulators using ordinary differential equation-based recursive optimization (RO) and information theory-based mutual information (MI), respectively. The dotted line without arrowhead denotes non-regulation (redundant), the dotted arrow denotes the indirect regulation (redundant) and the solid arrow denotes the true regulation. d We also analyzed key regulatory factors and key metabolic pathways which were closely related to the phase transition of Arabidopsis flowering development from the time of initiation to maturation time