Cepred: predicting the co-expression patterns of the human intronic microRNAs with their host genes.
Cepred: predicting the co-expression patterns of the human intronic microRNAs with their host genes.
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DOI：
10.1371/journal.pone.0004421
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发表时间：
2009
期刊：
影响因子：
3.7
通讯作者：
Cui, Qinghua
中科院分区：
文献类型：
--
作者：
Wang, Dong;Lu, Ming;Miao, Jing;Li, Tingting;Wang, Edwin;Cui, Qinghua
识别表达microRNA的组织可以增强对与该microRNA相关的功能，生物学过程和疾病的理解。然而，microRNA生物发生和表达的机制在很大程度上仍然不清楚，并且microRNA表达的组织的鉴定是有限的。在此，我们提出了一种基于机器学习的方法来预测内含子microRNA是否与其宿主基因表现出高共表达，通过这样做，我们可以通过其宿主基因的表达谱来推断microRNA在哪些组织中高表达。我们的方法是能够实现79%的留一交叉验证和95%的独立测试数据集的准确性。我们通过比较预测的组织特异性microRNA和生物学实验鉴定的组织特异性microRNA进一步评估了我们的方法。该研究为预测人类内含子microRNA与宿主基因的共表达模式提供了一个有价值的工具，也有助于理解microRNA的表达和调控机制。最后，这个框架可以很容易地扩展到其他物种。
Identifying the tissues in which a microRNA is expressed could enhance the understanding of the functions, the biological processes, and the diseases associated with that microRNA. However, the mechanisms of microRNA biogenesis and expression remain largely unclear and the identification of the tissues in which a microRNA is expressed is limited. Here, we present a machine learning based approach to predict whether an intronic microRNA show high co-expression with its host gene, by doing so, we could infer the tissues in which a microRNA is high expressed through the expression profile of its host gene. Our approach is able to achieve an accuracy of 79% in the leave-one-out cross validation and 95% on an independent testing dataset. We further estimated our method through comparing the predicted tissue specific microRNAs and the tissue specific microRNAs identified by biological experiments. This study presented a valuable tool to predict the co-expression patterns between human intronic microRNAs and their host genes, which would also help to understand the microRNA expression and regulation mechanisms. Finally, this framework can be easily extended to other species.
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影响因子：
56.9
作者：
Lagos-Quintana, M;Rauhut, R;Tuschl, T
通讯作者：
Tuschl, T
人类microRNA和疾病关联的分析。
影响因子：
3.7
作者：
Lu, Ming;Zhang, Qipeng;Deng, Min;Miao, Jing;Guo, Yanhong;Gao, Wei;Cui, Qinghua
通讯作者：
Cui, Qinghua
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14.9
作者：
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通讯作者：
Griffiths-Jones, S
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作者：
Jopling, CL;Yi, MK;Sarnow, P
通讯作者：
Sarnow, P
影响因子：
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作者：
Vasudevan, Shobha;Tong, Yingchun;Steitz, Joan A.
通讯作者：
Steitz, Joan A.