Bayesian error analysis model for reconstructing transcriptional regulatory networks -- Sun et al. 103 (21): 7988 Data Supplement - HTML Page - index.htslp -- Proceedings of the National Academy of Sciences

Sun et al. 10.1073/pnas.0600164103.

Supporting Information

Files in this Data Supplement:

Supporting Table 3
Supporting Figure 6
Supporting Table 4
Supporting Figure 7

Fig. 6. Convergence of MCMC iterations. The trace plots of the model parameters, p, q, and p assuming proper prior distributions. Other parameters display similar traces.

Supporting Figure 7

Fig. 7. The hierarchical clustering results based on protein-DNA binding intensities of 20 TFs whose bindings are specific to cell-cycle genes.

Table 3. Summary of model parameters

System model
Y	Relative gene expression levels
A	Transcriptional regulatory network matrix
a_ij	Stoichiometry coefficient for the pair of gene i and TF_j
R	Binary transcriptional regulatory network
B	Matrix of the observed binding intensities
b	Relative TF activities
N	Total number of genes
J	Total number of TFs
T	Total number of time points
e	Measurement error in gene expression data
Misclassification model	Observed
W	Binary binding network
p	Sensitivity of the observed binding data
q	Specificity of the observed binding data
Exposure model
p	Probability of r_ij = 1

Table 4. Twenty cell-cycle-related TFs

TF	FWER	Binding specificity	Rank in	TF	FWER	Binding specificity	Rank in
TF	P	P	specificity	TF	P	P	specificity
SWI4	0	9.47E-35	1	ACE2	0	7.18E-03	37
FKH2	0	2.62E-32	2	RGM1	0	7.29E-03	38
SWI6	0	1.47E-29	3	GAT3	0	1.36E-02	49
MBP1	0	2.53E-28	4	GAL4	0	2.36E-02	62
NDD1	0	5.76E-18	5	DIG1	0	2.56E-02	64
MCM1	0	1.81E-15	7	MAL13	0.0112	2.15E-07	14
SWI5	0	1.05E-12	8	IXR1	0.0112	6.01E-02	96
STB1	0	3.08E-09	10	CIN5	0.0336	7.88E-08	11
FKH1	0	1.86E-07	13	STE12	0.0448	3.10E-04	22
MET4	0	6.20E-04	23	YAP5	0.0672	3.44E-03	30

The FWER (family wise error rate) columns show the statistical significance that each TF is related to the yeast cell-cycle-gene expression data. Binding specificity summarizes the statistical evidence that the binding patterns of each pattern are related to cell-cycle genes. Rank in specificity shows the rank of the relevance to cell-cycle genes among all of the TFs studied in Lee et al. (1).

1. Lee, T. I., Rinaldi, N. J., Robert, F., Odom, D. T., Bar-Joseph, Z., Gerber, G. K., Hannett, N. M., Harbison, C. T., Thompson, C. M., Simon, I., et al. (2002) Science 298, 799-804.