Root stem cell niche GRN models. Nodes represent the genes or hormones in the case of auxin. Arrows correspond to activations, and flat arrows correspond to repressions. Four models were tested. Model A and A' (a) differ from B and B' (b) in the WOX5 negative regulation. In models A and A', WOX5 is downregulated by MGP, whereas in models B and B' WOX5 is downregulated by the hypothetical gene CLEX. Models A' and B' differ from models A and B in the SCR value in line 14 of their logical rule as shown in Additional file 1. In (c), the GRN used for the coupled GRN model is depicted. Even when CLE40 is an experimentally reported data, in our model, we assume negative regulation of WOX5 in all SCs, so CLEX is treated as a novel prediction. In all GRNs, red arrows indicate the novel postulated interactions, and black arrows indicate interactions based on experimental data. Purple nodes in (c) are the nodes involved in the activator-inhibitor motif. The IAA node in the GRN graph represents the Aux/IAA gene family, not auxin. Of all the interaction considered here, the dimer SHR/SCR activating SCR and MGP, auxin repressing Aux/IAA and Aux/IAA repressing ARF had been experimentally confirmed as direct interactions.