The area of stem cell research is rapidly evolving. One of the recent achievements is the capture of naïve human embryonic stem cells through reprogramming of primed human embryonic stem cells. In this thesis, Gene Co-expression Networks are used to further our understanding of naïve and primed human embryonic (hESCs). We found that GCNs of naïve and primed hESCs exhibits distinct network topological structures. Rewiring analysis of naïve and primed hESC GCNs showed significant rewiring and

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... ge in networks structures and behaviors. This demonstrates that naïve and primed hESCs are distinct cellular states. In addition, KLF genes circuitry, NANOG, and SOX2 were more active in naïve GCNs and formed more edges with other genes. Those genes were significantly rewired in our GCNs. We found that KLF5 is major player in our naïve hESCs GCNs. In addition, NANOG and SOX2 interacted only in naïve hESCs GCNs..The observations in our GCNs concerning KLF circuitry activity and, NANOG and SOX2 interactions were consistent with published stem cell literature. This demonstrates the power of GCNs in unfolding cellular characteristics and understanding the underlying gene dynamics.