Analysis of gene expression in different cell types

Cellular states are plastic, and even terminally differentiated cells can be reprogrammed to pluripotency by ectopic expression of selected transcription factors, yet it remains inefficient in practice. Cell reprogramming is remarkable for its potential to impact research and therapies because induced pluripotent stem (iPS) cells are similar to embryo stem (ES) cells in many aspects so that they are suitable substitute for ES cells. Since distinct gene expression pattern is one of the most important features of specific cell state, we analyze the relationship between gene expression and the cell state. In this paper, we chose human ES cells, iPS cells, and fibroblasts to compare. Our results show that iPS cells have an ES cell-like expression pattern and suggest that those genes which have distinct expression intensities in different cell states perform significant function in cell fate regulation. What's more, genome-wide occupancy maps have revealed the correlation between the ectopic expression factors and the gene expression intensities.