Integrative view of the OCT4 regulatory network (Use Case #1, Study 2).

Abstract

<p>(<b>A</b>) Gene regulatory modular network of OCT4 transcription factor. Grey boxes represent the gene regulatory and co-expressed modules; rectangles represent the genes; red rectangles, the genes with known binding sites; a yellow triangle, the transcription factor; blue edges, TF-target gene relationships; red lines, co-expressed TF-gene pairs. The top module (shown in <b>C</b>), called ‘Module 1′, is highlighted. (<b>B</b>) GenomeBrowser window showing the sequences of the genes and TF binding sites. The OCT4 binding site for the selected in the network (<b>A</b>) <i>Pou2f1</i> gene is shown. (<b>C</b>) Module Table showing the gene modules, TFs, and functional annotation for each module with Fisher enrichment score (p-value) of GO terms. The top ‘Module 1′ is highlighted. (<b>D</b>) Table of TFs and target genes found in public databases. Gene <i>Pou2f1</i> (selected in <b>A</b>) is highlighted in magenta. (<b>E</b>) Multi-Experiment Viewer represents the matrix of genes (in columns) co-expressed with the query gene(s) in microarray experiments (in rows). (<b>F</b>) Microarray Gene Expression window showing the hit map and hierarchical tree of clustering data from selected experiments. Pointing out the mouse on the tree vertex shows the significant GO terms for the cluster; ‘Module 1′ is highlighted.</p