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1.
Figure 4

Figure 4. The ERα-centered core regulatory module structure.. From: Hierarchical Modularity in ER? Transcriptional Network Is Associated with Distinct Functions and Implicates Clinical Outcomes.

The hub nodes were selected based on their respective occurrence frequency of transcription binding activities, identified from the time-series ChIP-seq data sets, together with the manually-selected ones, which have already been validated and acknowledged in experiments and literatures published recently. The red edges denote positive activation, and dashed blue ones denote negative inhibition.

Binhua Tang, et al. Sci Rep. 2012;2:875.
2.
Figure 5

Figure 5. The structure of the embedded Module I (ERα-GATA3-XBP1-MYC).. From: Hierarchical Modularity in ER? Transcriptional Network Is Associated with Distinct Functions and Implicates Clinical Outcomes.

The subplots illustrate gene expression patterns and corresponding SNR values for those module components. Module I contains only one self-inhibition loop (XBP1). And the corresponding time-course gene expression plots and inherent expression patterns are given in right panels, together with the up-/down-regulated information (+/−) for each gene on the rightmost column of the bottom plot. MYC and XBP1 are up-regulated in the module.

Binhua Tang, et al. Sci Rep. 2012;2:875.
3.
Figure 6

Figure 6. The structure of the embedded Module II (ERα-CEBP-AP1-GATA3-SP1-FOXA1).. From: Hierarchical Modularity in ER? Transcriptional Network Is Associated with Distinct Functions and Implicates Clinical Outcomes.

The subplots illustrate the gene expression patterns and corresponding SNR values for those module components. Module II mainly contains feed-forward loops, while only one bi-span (ERα-CEBP:AP1-SP1) and self-inhibition loop (SP1). And the corresponding time-course gene expression plots and inherent expression patterns are given in right panels, together with the up-/down-regulated information (+/−) for each gene on the rightmost column of the bottom plot. All genes are down-regulated in the module.

Binhua Tang, et al. Sci Rep. 2012;2:875.
4.
Figure 7

Figure 7. The structure of the embedded Module III (ERα-XBP1-NFκB-OCT1-PAX2).. From: Hierarchical Modularity in ER? Transcriptional Network Is Associated with Distinct Functions and Implicates Clinical Outcomes.

The subplots illustrate gene expression patterns and corresponding SNR values for those module components. Module III mainly contains four bi-span loops, self-inhibition loops (NFκB, OCT1 and XBP1) and one co-inhibitory loop (XBP1 and NFκB). And the corresponding time-course gene expression plots and inherent expression patterns are given in right panels, together with the up-/down-regulated information (+/−) for each gene node on the rightmost column of the bottom plot. XBP1 is up-regulated, and NFκB is down-regulated in Module III.

Binhua Tang, et al. Sci Rep. 2012;2:875.
5.
Figure 1

Figure 1. The computational analysis flowchart for inferring ERα transcription regulatory network.. From: Hierarchical Modularity in ER? Transcriptional Network Is Associated with Distinct Functions and Implicates Clinical Outcomes.

It contains two major sections, one is for data processing and the other is for network and modularity analyses. The first section includes ChIP-seq data mapping and peak-calling, correlating ChIP-seq with microarray gene expression data, and Bayesian multivariate modeling for network inference. The second section covers analysis on the inferred network and modularity, the corresponding gene ontology (GO) analysis, and patient survival analysis on the network modules based on three clinical data sets published recently.

Binhua Tang, et al. Sci Rep. 2012;2:875.
6.
Figure 3

Figure 3. The ERα transcription regulatory network structure and related analysis at time 4 hours.. From: Hierarchical Modularity in ER? Transcriptional Network Is Associated with Distinct Functions and Implicates Clinical Outcomes.

(A) The inferred ERα transcription regulatory network structure at time 4 hours. The red edges denote positive activation, and dashed blue edges denote negative inhibition. (B) The hierarchical topological structure of the inferred ERα transcription regulatory network at time 4 hours. (C) and (D) illustrate the connectivity distribution, Pearson correlation and p-value distributions (between the regulatory coefficients and SNRs) as the functions of absolute rank value of regulatory strength for the network structure at time 4 hours. The plots for other time points, i.e. 0, 1, and 24 hours are given in the Supplemental Figures S4–S6.

Binhua Tang, et al. Sci Rep. 2012;2:875.
7.
Figure 9

Figure 9. The Kaplan-Meier survival analysis based on the target genes regulated by the three modules.. From: Hierarchical Modularity in ER? Transcriptional Network Is Associated with Distinct Functions and Implicates Clinical Outcomes.

The clinical survival information of 337 breast cancer patients is selected from van de Vijver et al.4142. The subplot (A) gives the statiscally siginificant result between the patient groups PG:3 vs PG:4 (Module I), and their corresponding group estrogen receptor status and survival stage (grade) information are also provided on the left bottom (log-rank test p-value: 0.0044178). The subplots (B) and (C) depict the analysis results on the patient groups PG:2 vs PG:4 (Module II), and PG:1 vs PG:4 (Module III), respectively.

Binhua Tang, et al. Sci Rep. 2012;2:875.
8.
Figure 8

Figure 8. The statistical analysis of the regulated genes by Module III across the four time points.. From: Hierarchical Modularity in ER? Transcriptional Network Is Associated with Distinct Functions and Implicates Clinical Outcomes.

(A) The subplots ilustrate the regulated gene expression by Module III at each time, respectively. At time 0 hour, Module III directly regulates the 355 genes; at 1 hour, Module III regulates 583 genes; for time 4 hours, the regulated genes fall down to 522, and 335 at time 24 hours. (B) The right panel depicts the association matrix of those gene regulated by Module III across the four time points, the diagonal entries denote the individual gene number regulated by Module III across all four time points, and off-diagonal entries denote common gene number (percentage) between the corresponding two time points.

Binhua Tang, et al. Sci Rep. 2012;2:875.
9.
Figure 2

Figure 2. The selection of optimal parameters for the ERα ChIP-seq data at time point 0 hour.. From: Hierarchical Modularity in ER? Transcriptional Network Is Associated with Distinct Functions and Implicates Clinical Outcomes.

A distribution of peak numbers (the upper panel) and FDR (the lower panel) vs. the p-threshold (A). A track rate distribution for peak number and FDR with respect to the interval number N (B). The global peak number and FDR distributions, track rate distributions for peak number and FDR plots at other time points are given in the Supplemental Figures S1–3. C and D. The identification of TF hubs according to the occurrence frequency of those candidates (C). The percentages denote the corresponding occurrence distribution among all candidates identified from the time-series ChIP-seq data. TF candidates' pairwise intersection matrix across all the four time points (D). The diagonal entries denote the candidate counts at the corresponding time points, and other non-diagonal entries denote those candidate counts of intersection identified between any two different time points.

Binhua Tang, et al. Sci Rep. 2012;2:875.

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