An efficient weighted graph strategy to identify differentiation associated genes in embryonic stem cells.
An efficient weighted graph strategy to identify differentiation associated genes in embryonic stem cells.
复制标题
识别胚胎干细胞分化相关基因的有效加权图策略
DOI：
10.1371/journal.pone.0062716
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发表时间：
2013
期刊：
影响因子：
3.7
通讯作者：
Li J
中科院分区：
文献类型：
--
作者：
Zhang J;Li L;Peng L;Sun Y;Li J
在过去的几十年里，胚胎干细胞（ESCs）作为研究早期发育过程的模型系统，并由于其在再生医学中的潜在治疗应用而引起了极大的兴趣。然而，ESC分化的潜在机制仍不清楚，这限制了我们对干细胞治疗潜力的探索。幸运的是，生物数据集的数量和多样性的增加为我们提供了探索生物秘密的机会。然而，利用多样化的生物信息来促进ESC研究的进展仍然是一个挑战。在这里，我们提出了一个可扩展的，高效的和灵活的功能预测框架，集成了不同的生物信息，使用一个简单的加权策略，揭示小鼠ESC分化的遗传决定因素。这种方法的优点是，它可以进行预测的基础上动态信息融合，由于简单的加权策略。通过这种方法，我们确定了30个基因，据报道与干细胞分化有关，我们认为这些基因与胚胎干细胞的分化或多能性有关。我们还预测了70个基因作为有助于分化的候选基因，这需要进一步确认。总体而言，我们的研究结果表明，这种策略可以作为一个有用的工具，ESC的研究。
In the past few decades, embryonic stem cells (ESCs) were of great interest as a model system for studying early developmental processes and because of their potential therapeutic applications in regenerative medicine. However, the underlying mechanisms of ESC differentiation remain unclear, which limits our exploration of the therapeutic potential of stem cells. Fortunately, the increasing quantity and diversity of biological datasets can provide us with opportunities to explore the biological secrets. However, taking advantage of diverse biological information to facilitate the advancement of ESC research still remains a challenge. Here, we propose a scalable, efficient and flexible function prediction framework that integrates diverse biological information using a simple weighted strategy, for uncovering the genetic determinants of mouse ESC differentiation. The advantage of this approach is that it can make predictions based on dynamic information fusion, owing to the simple weighted strategy. With this approach, we identified 30 genes that had been reported to be associated with differentiation of stem cells, which we regard to be associated with differentiation or pluripotency in embryonic stem cells. We also predicted 70 genes as candidates for contributing to differentiation, which requires further confirmation. As a whole, our results showed that this strategy could be applied as a useful tool for ESC research.
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DOI：
10.1016/s0097-8485(96)80004-0
发表时间：
1996-03-01
期刊：
COMPUTERS & CHEMISTRY
影响因子：
--
作者：
Gribskov, M;Robinson, NL
通讯作者：
Robinson, NL
影响因子：
4.3
作者：
Bar-On, Ortal;Shapira, Ma'anit;Hershko, Dan D.
通讯作者：
Hershko, Dan D.
影响因子：
11.4
作者：
Feinberg, Mark W.;Wara, Akm Khyrul;Jain, Mukesh K.
通讯作者：
Jain, Mukesh K.
影响因子：
14.9
作者：
Chatr-aryamontri, Andrew;Ceol, Arnaud;Palazzi, Luisa Montecchi;Nardelli, Giuliano;Schneider, Maria Victoria;Castagnoli, Luisa;Cesareni, Gianni
通讯作者：
Cesareni, Gianni
DOI：
10.1073/pnas.0711613105
发表时间：
2008-02-05
影响因子：
11.1
作者：
Liu, Suling;Ginestier, Christophe;Wicha, Max S.
通讯作者：
Wicha, Max S.