An organogenesis network-based comparative transcriptome analysis for understanding early human development in vivo and in vitro.
An organogenesis network-based comparative transcriptome analysis for understanding early human development in vivo and in vitro.
复制标题
基于器官发生网络的比较转录组分析，用于了解早期人类体内和体外发育。
DOI：
10.1186/1752-0509-5-108
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发表时间：
2011-07-06
影响因子：
--
通讯作者：
Wang K
中科院分区：
文献类型：
--
作者：
Fang H;Jin W;Yang Y;Jin Y;Zhang J;Wang K
综合网络在各种情况下都大有希望。在最近的一项研究中，我们结合了表达和相互作用的数据，以确定一个假定的网络基础早期人类器官发生，其中包含两个模块，干相关模块（hStemModule）和分化相关模块（hDiffModule）。然而，由于其假设的性质，目前还不清楚这个网络是否允许比较转录组分析，以促进我们对早期人类发育的理解，无论是在体内还是体外。基于这个集成网络，我们在这里报告与来自各种来源的上下文依赖性转录组数据的比较。通过将网络及其两个模块视为基因集并进行基因集富集分析，我们证明了网络作为干潜力与分化潜力的定量监测器的实用性。在早期人类器官发生期间，hStemModule反映了干细胞潜能逐渐丧失的一般性。hDiffModule指示阶段特异性分化潜力，因此不适合描绘延长的发育窗口。对不同类型的培养细胞的处理进一步揭示了hStemModule是根据其干细胞潜能区分不同细胞类型的通用指标。相比之下，hDiffModule不能区分不同类型的分化细胞，但能够预测不同来源的多能细胞的分化潜力的差异。我们还观察到这两个模块和早期胚状体（EBs），这是在体外分化模型之间的显着正相关。尽管如此，面向网络的比较显示，随着时间的推移，发育中的胚胎和体外培养的EB之间存在相当大的差异，以试图模仿体内过程。我们强烈建议使用这两个模块，无论是当涉及不同来源的多能细胞类型时，还是当所做的比较仅限于早期人体器官发生过程中的体内胚胎（以及等效的体外分化模型）时。基于网络的比较转录组分析将有助于增加有关人类胚胎发生的知识，特别是当目前只有转录组数据可用时。这些进步将为网络应用增加一个额外的维度。
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. 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. Processing of cultured cells of different types further revealed that the hStemModule is a general indicator that distinguishes different cell types in terms of their stem potential. In contrast, the hDiffModule cannot distinguish between differentiated cells of different types but is able to predict differences in the differentiation potential of pluripotent cells of different origins. We also observed a significant positive correlation between each of these two modules and early embryoid bodies (EBs), which are used as in vitro differentiation models. Despite this, the network-oriented comparisons showed considerable differences between the developing embryos and the EBs that were cultured in vitro over time to try to mimic in vivo processes. We strongly recommend the use of these two modules either when pluripotent cell types of different origins are involved or when the comparisons made are constrained to the in vivo embryos during early human organogenesis (and an equivalent in vitro differentiation models). Network-based comparative transcriptome analysis will contribute to an increase in knowledge about human embryogenesis, particularly when only transcriptome data are currently available. These advances will add an extra dimension to network applications.
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影响因子：
--
作者：
Lin CC;Hsiang JT;Wu CY;Oyang YJ;Juan HF;Huang HC
通讯作者：
Huang HC
影响因子：
64.5
作者：
Kumar, Dhiraj;Nath, Lekha;Rao, Kanury V. S.
通讯作者：
Rao, Kanury V. S.
影响因子：
14.9
作者：
Barrett T;Troup DB;Wilhite SE;Ledoux P;Rudnev D;Evangelista C;Kim IF;Soboleva A;Tomashevsky M;Marshall KA;Phillippy KH;Sherman PM;Muertter RN;Edgar R
通讯作者：
Edgar R
DOI：
10.1111/j.2517-6161.1995.tb02031.x
发表时间：
1995-01-01
影响因子：
5.8
作者：
BENJAMINI, Y;HOCHBERG, Y
通讯作者：
HOCHBERG, Y
影响因子：
3.5
作者：
Dobson, AT;Raja, R;Pera, RAR
通讯作者：
Pera, RAR