Figure 7. Application of MERLIN to differentiation time course of human ES to neural precursor cells identifies two large modules with opposite patterns of expression.

A. Shown are the two modules, Modules 1, and 7, that exhibit characteristic temporal patterns of expression together with their predicted regulators from MERLIN and regulators whose ChIP-seq targets are enriched in the module. Known pluripotency maintenance regulators (POU5F1), and predicted neural fate driver genes are shown in larger fonts. B. Predicted targets of POU5F1 using MERLIN. * denotes membership in Module 1, which we associate with maintenance of ES state. MERLIN can infer both repressive and activating relationships between TF and target genes, e.g. CCDC11 and POU5F1. We also show ChIP-seq (Red column, NANOG-ChIP, [44]) and ChIP-chip datasets (Magenta columns, SOX2-OCT4-NANOG targets from Boyer et al., [71]) C. Predicted targets of DUSP5 using MERLIN. Some DUSP5 targets are also occupied by NANOG transcription factor.