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Cell-Type-Specific Predictive Network Yields Novel Insights into Mouse Embryonic Stem Cell Self-Renewal and Cell Fate

Figure 4

Data Visualization for Mining mESC Self-Renewal Gene Predictions.

A. Views of Tdh-centric networks created using our StemSight Scout visualization tool, available at StemSight.org. Adjusting Scout network views to display only edges with inference scores of 0.5 and 0.9997 show that the novel gene Tdh is tightly connected to many well-known self-renewal genes in our training gold standard, including Pou5f1, Sox2, Nanog, Nr0B1, and Phc1. B. Supporting edge info for the TdhPou5f1 edge. Supporting edge information shows that this edge is supported by several protein-DNA interaction (PDI) assays as well as gene expression datasets from a study investigating mESC cell differentiation in different mESC cell lines. For supporting edge detail between Tdh and other gold standard genes, see Figure S5 or explore the Tdh interactome online at StemSight.org/scout. C. SPELL for StemSight Search Results. From a supporting edge information window, you can drill down to the individual gene expression levels in microarray datasets. This view shows how expression data reveals rank-ordered correlations observed between Tdh and gold standard genes Gbf3, Fbxo15, Nr0b1, Phc1, Pou5f1, and Sox2.

Figure 4

doi: https://doi.org/10.1371/journal.pone.0056810.g004