Dynamic epigenetic mode analysis using spatial temporal clustering.
BACKGROUND
Differentiation of human embryonic stem cells requires precise control of gene expression that depends on specific spatial and temporal epigenetic regulation. Recently available temporal epigenomic data derived from cellular differentiation processes provides an unprecedented opportunity for characterizing fundamental properties of epigenomic dynamics and revealing regulatory roles of epigenetic modifications.


RESULTS
This paper presents a spatial temporal clustering approach, named STCluster, which exploits the temporal variation information of epigenomes to characterize dynamic epigenetic mode during cellular differentiation. This approach identifies significant spatial temporal patterns of epigenetic modifications along human embryonic stem cell differentiation and cluster regulatory sequences by their spatial temporal epigenetic patterns.


CONCLUSIONS
The results show that this approach is effective in capturing epigenetic modification patterns associated with specific cell types. In addition, STCluster allows straightforward identification of coherent epigenetic modes in multiple cell types, indicating the ability in the establishment of the most conserved epigenetic signatures during cellular differentiation process.
School of Computer Science and Technology, Donghua University, Shanghai, China.
YangLan
Y
Gan
Department of Computer Science and Technology, Tongji University, Shanghai, China.
Han
H
Tao
School of Computer Engineering and Science, Shanghai University, Shanghai, China.
Guobing
G
Zou
School of Computer Science and Technology, Donghua University, Shanghai, China.
Cairong
C
Yan
Department of Computer Science and Technology, Tongji University, Shanghai, China. jhguan@tongji.edu.cn.
Jihong
J
Guan
D002454:Cell Differentiation / Q000235:genetics*; D016000:Cluster Analysis; D019175:DNA Methylation; D053595:Embryonic Stem Cells / Q000378:metabolism / Q000502:physiology*; D044127:Epigenesis, Genetic; D018507:Gene Expression Regulation, Developmental; D006657:Histones / Q000378:metabolism; D006801:Humans
D006657:Histones
Cellular differentiation; Dynamic epigenetic mode; Epigenetic modification; Spatial temporal clustering