This article is part of the supplement: Proceedings of the 2009 AMIA Summit on Translational Bioinformatics .

Proceedings

A systems biology approach to the identification and analysis of transcriptional regulatory networks in osteocytes

Angela K Dean¹ , Stephen E Harris^2,3 , Ivo Kalajzic⁴ and Jianhua Ruan¹

¹Department of Computer Science, The University of Texas at San Antonio, San Antonio, TX 78249, USA

²Department of Periodontics, The University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA

³Department of Cellular and Structural Biology, The University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA

⁴Department of Reconstructive Sciences, University of Connecticut Health Center, Farmington, CT06030, USA

author email corresponding author email

BMC Bioinformatics 2009, 10(Suppl 9):S5doi:10.1186/1471-2105-10-S9-S5

Published:	17 September 2009

Abstract

Background

The osteocyte is a type of cell that appears to be one of the key endocrine regulators of bone metabolism and a key responder to initiate bone formation and remodeling. Identifying the regulatory networks in osteocytes may lead to new therapies for osteoporosis and loss of bone.

Results

Using microarray, we identified 269 genes over-expressed in osteocyte, many of which have known functions in bone and muscle differentiation and contractility. We determined the evolutionarily conserved and enriched TF binding sites in the 5 kb promoter regions of these genes. Using this data, a transcriptional regulatory network was constructed and subsequently partitioned to identify cis-regulatory modules.

Conclusion

Our results show that many osteocyte-specific genes, including two well-known osteocyte markers DMP1 and Sost, have highly conserved clustering of muscle-related cis-regulatory modules, thus supporting the concept that a muscle-related gene network is important in osteocyte biology and may play a role in contractility and dynamic movements of the osteocyte.