Transcriptional Co-Expression Analysis of Embryonic Stem Cells

Abstract

The decision between differentiation and self-renewal of embryonic stem cells (ESCs) are controlled by a complex network formed by interacting genes or proteins. Identifying critical components of this regulatory network and exploring their behavior patterns is crucial towards understanding the underlying mechanisms controlling ESC differentiation and realizing their potentials in regenerative medicine. In this chapter, we describe the usage of co-expression analysis in identifying conserved and divergent genomic, transcriptomic, and network modules critical for the earliest stage of ESCs differentiation.

Keywords: Co-expression, cell cycle, transcriptome mapping, chromosomal domains, embryonic stem cell, embryonic bodies, comparative transcriptomics, transcriptional module, LIF, FGF, Nodal, Wnt, BMP, TGF-β, Oct4, Sox2, nanog, JAK/STAT, pluripotency.