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Table 1 The 46 prior connections and the connections inferred from the linear ODE model and Markov model

From: Inference of the Xenopus tropicalis embryonic regulatory network and spatial gene expression patterns

Prior information Linear ODE model Linear Markov model
sox17a regulates hnf1b Inferred Inferred
sox17a regulates foxa4a Inferred Inferred
sox17a regulates foxa1 Inferred Inferred
sox17a regulates foxa2 Inferred Inferred
sox17a regulates gata4 Inferred  
sox17a regulates gata5 Inferred  
sox17a regulates gata6 Inferred Inferred
sox17a regulates bix1.2 Inferred  
sox17b.1 regulates hnf1b Inferred Inferred
sox17b.1 regulates foxa4a   Inferred
sox17b.1 regulates foxa1 Inferred Inferred
sox17b.1 regulates foxa2 Inferred Inferred
sox17b.1 regulates gata4 Inferred  
sox17b.1 regulates gata5 Inferred Inferred
sox17b.1 regulates gata6 Inferred Inferred
sox17b.1 regulates bix1.2 Inferred Inferred
sox7 regulates sox17a   
sox7 regulates sox17b.1   
gata4 regulates sox17a   
gata4 regulates sox17b.1   Inferred
gata5 regulates sox17a   Inferred
gata5 regulates sox17b.1 Inferred Inferred
gata6 regulates sox17a Inferred  
gata6 regulates sox17b.1   
bix1.2 regulates sox17a Inferred Inferred
bix1.2 regulates sox17b.1 Inferred  
vegt regulates mix1 Inferred  
vegt regulates mixer Inferred  
vegt regulates sox17a   Inferred
vegt regulates sox17b.1 Inferred Inferred
foxh1 regulates otx2 Inferred Inferred
foxh1 regulates lhx1 Inferred Inferred
foxh1 regulates mix1 Inferred Inferred
foxh1 regulates mixer Inferred Inferred
foxh1 regulates bix1.2 Inferred Inferred
foxh1 regulates t   
foxh1 regulates ventx2.2   Inferred
foxh1 regulates sox17a Inferred Inferred
foxh1 regulates sox17b.1 Inferred  
foxh1 regulates frzb Inferred Inferred
foxh1 regulates gsc   Inferred
foxh1 regulates hhex Inferred Inferred
foxh1 regulates msx1 Inferred Inferred
ventx2.2 regulates ventx1.2 Inferred Inferred
ventx1.2 regulates myf5 Inferred Inferred
t regulates myf5   Inferred
  1. The blank stands for missing edges in the inferred networks. There are 34 and 32 connections same as the prior information in the networks inferred from the linear ODE model and Markov model, respectively. Among these connections, 25 connections are shared. Note that the prior information we provide to the algorithm is only the existence/non-existence of interactions, not including their information about activation or inhibition.