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

Zheng, Zhenzhen; Christley, Scott; Chiu, William T; Blitz, Ira L; Xie, Xiaohui; Cho, Ken WY; Nie, Qing

doi:10.1186/1752-0509-8-3

BMC Systems Biology

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

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.

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ISSN: 1752-0509

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