原创力文档an organogenesis network-based comparative transcriptome analysis for understanding early human development in vivo and in vitro一个器官形成网络比较转录组分析对于理解早期人类发展体内和体外.pdfVIP
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an organogenesis network-based comparative transcriptome analysis for understanding early human development in vivo and in vitro一个器官形成网络比较转录组分析对于理解早期人类发展体内和体外
An organogenesis network-based comparative
transcriptome analysis for understanding early
human development in vivo and in vitro
Fang et al.
Fang et al. BMC Systems Biology 2011, 5:108
/1752-0509/5/108 (6 July 2011)
Fang et al. BMC Systems Biology 2011, 5:108
/1752-0509/5/108
RESEARCH ARTICLE Open Access
An organogenesis network-based comparative
transcriptome analysis for understanding early
human development in vivo and in vitro
Hai Fang 1,2,3†, Wen Jin1†, Ying Yang2,4, Ying Jin2,4, Ji Zhang1,2* and Kankan Wang1,2*
Abstract
Background: Integrated networks hold great promise in a variety of contexts. In a recent study, we have
combined expression and interaction data to identify a putative network underlying early human organogenesis
that contains two modules, the stemness-relevant module (hStemModule) and the differentiation-relevant module
(hDiffModule). However, owing to its hypothetical nature, it remains unclear whether this network allows for
comparative transcriptome analysis to advance our understanding of early human development, both in vivo and
in vitro.
Results: Based on this integrated network, we here report comparisons with the context-dependent transcriptome
data from a variety of sources. By viewing the network and its two modules as gene sets and conducting gene set
enrichment analysis, we demonstrate the network’s utility as a quantitative monitor of the stem potential versus the
differentiation potential. During early human organogenesis, the hStemModule reflects the generality of a gradual
loss of the stem potential. The hDiffModule indicates the stage-specific differentiation potential and is therefore not
suitable for depicting an extended developmental window
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