Analysis of regulatory network involved in mechanical induction of embryonic stem cell differentiation.

PloS One
Xinan ZhangIpsita Banerjee

Abstract

Embryonic stem cells are conventionally differentiated by modulating specific growth factors in the cell culture media. Recently the effect of cellular mechanical microenvironment in inducing phenotype specific differentiation has attracted considerable attention. We have shown the possibility of inducing endoderm differentiation by culturing the stem cells on fibrin substrates of specific stiffness. Here, we analyze the regulatory network involved in such mechanically induced endoderm differentiation under two different experimental configurations of 2-dimensional and 3-dimensional culture, respectively. Mouse embryonic stem cells are differentiated on an array of substrates of varying mechanical properties and analyzed for relevant endoderm markers. The experimental data set is further analyzed for identification of co-regulated transcription factors across different substrate conditions using the technique of bi-clustering. Overlapped bi-clusters are identified following an optimization formulation, which is solved using an evolutionary algorithm. While typically such analysis is performed at the mean value of expression data across experimental repeats, the variability of stem cell systems reduces the confidence on such ana...Continue Reading

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Citations

Apr 11, 2013·Journal of Biological Engineering·Joseph CandielloIpsita Banerjee
Feb 9, 2013·Chemical Reviews·Akon HiguchiAkihiro Umezawa
Feb 5, 2014·Nanomedicine : Nanotechnology, Biology, and Medicine·Yu-Wei ChiuYi-Lwun Ho

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Methods Mentioned

BETA
PCR

Software Mentioned

Gene Set Enrichment Analysis ( GSEA )
GSEA

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