title: Transcriptome coexpression map of human embryonic stem cells.
abstract: BACKGROUND
  Human embryonic stem (ES) cells hold great promise for medicine and science. The transcriptome of human ES cells has been studied in detail in recent years. However, no systematic analysis has yet addressed whether gene expression in human ES cells may be regulated in chromosomal domains, and no chromosomal domains of coexpression have been identified.
  
  
  RESULTS
  We report the first transcriptome coexpression map of the human ES cell and the earliest stage of ES differentiation, the embryoid body (EB), for the analysis of how transcriptional regulation interacts with genomic structure during ES self-renewal and differentiation. We determined the gene expression profiles from multiple ES and EB samples and identified chromosomal domains showing coexpression of adjacent genes on the genome. The coexpression domains were not random, with significant enrichment in chromosomes 8, 11, 16, 17, 19, and Y in the ES state, and 6, 11, 17, 19 and 20 in the EB state. The domains were significantly associated with Giemsa-negative bands in EB, yet showed little correlation with known cytogenetic structures in ES cells. Different patterns of coexpression were revealed by comparative transcriptome mapping between ES and EB.
  
  
  CONCLUSIONS
  The findings and methods reported in this investigation advance our understanding of how genome organization affects gene expression in human ES cells and help to identify new mechanisms and pathways controlling ES self-renewal or differentiation.
authors: Bioinformatics Unit, Branch of Research Resources, National Institute on Aging, NIH, Baltimore, MD 21224, USA. huaili@mail.nih.gov
authors: Huai
authors: H
authors: Li
authors: Ying
authors: Y
authors: Liu
authors: Soojung
authors: S
authors: Shin
authors: Yu
authors: Y
authors: Sun
authors: Jeanne F
authors: JF
authors: Loring
authors: Mark P
authors: MP
authors: Mattson
authors: Mahendra S
authors: MS
authors: Rao
authors: Ming
authors: M
authors: Zhan