A novel representation of RNA secondary structure based on element-contact graphs.
A novel representation of RNA secondary structure based on element-contact graphs.
复制标题
基于元素接触图的 RNA 二级结构的新颖表示
DOI：
10.1186/1471-2105-9-188
复制
发表时间：
2008-04-11
影响因子：
3
通讯作者：
Wang S
中科院分区：
文献类型：
--
作者：
Shu W;Bo X;Zheng Z;Wang S
背景非编码RNA（noncoding RNA，ncRNA）以其独特的结构在许多生物学过程中发挥着重要作用。基于RNA图的拓扑指数可以用于RNA的比较、识别和分类，近年来又引起了人们的兴趣。虽然拓扑指数描述了RNA二级结构的主要拓扑特征，但在一定程度上忽略了RNA结构的细节信息。因此，它是必要的，以确定低退化的拓扑特征的基础上完整的和细粒度的RNA图形representations.ResultsIn这项研究中，我们提出了一个完整的和精细的计划，RNA图形表示作为一个新的基础上构建RNA拓扑指数。我们提出了一个三个顶点加权的元素接触图（ECG）的组合来描述RNA二级结构中的RNA元素细节及其相邻模式。茎和环拓扑结构都在ECG中完全编码。从6，305个ncRNA数据集中研究了由ECG定义的三个典型拓扑指数家族与RNA二级结构之间的关系。拓扑指数的适用性说明了三个应用案例研究。基于应用的小数据集，我们发现，拓扑指数可以区分真正的pre-miRNAs与伪pre-miRNAs的准确率约为96%，并可以聚类已知类型的ncRNAs的准确率约为98%，respectively.ConclusionThe结果表明，拓扑指数可以表征RNA结构的细节，并可能有潜在的作用，在识别和分类ncRNAs。此外，这些指标可能会导致一种新的方法来发现新的ncRNA。然而，需要进一步的研究来完全解决预测和分类非编码RNA的挑战性问题。
BackgroundDepending on their specific structures, noncoding RNAs (ncRNAs) play important roles in many biological processes. Interest in developing new topological indices based on RNA graphs has been revived in recent years, as such indices can be used to compare, identify and classify RNAs. Although the topological indices presented before characterize the main topological features of RNA secondary structures, information on RNA structural details is ignored to some degree. Therefore, it is necessity to identify topological features with low degeneracy based on complete and fine-grained RNA graphical representations.ResultsIn this study, we present a complete and fine scheme for RNA graph representation as a new basis for constructing RNA topological indices. We propose a combination of three vertex-weighted element-contact graphs (ECGs) to describe the RNA element details and their adjacent patterns in RNA secondary structure. Both the stem and loop topologies are encoded completely in the ECGs. The relationship among the three typical topological index families defined by their ECGs and RNA secondary structures was investigated from a dataset of 6,305 ncRNAs. The applicability of topological indices is illustrated by three application case studies. Based on the applied small dataset, we find that the topological indices can distinguish true pre-miRNAs from pseudo pre-miRNAs with about 96% accuracy, and can cluster known types of ncRNAs with about 98% accuracy, respectively.ConclusionThe results indicate that the topological indices can characterize the details of RNA structures and may have a potential role in identifying and classifying ncRNAs. Moreover, these indices may lead to a new approach for discovering novel ncRNAs. However, further research is needed to fully resolve the challenging problem of predicting and classifying noncoding RNAs.
登录
查看更多内容
影响因子：
4.5
作者：
Gevertz, J;Gan, HH;Schilick, T
通讯作者：
Schilick, T
DOI：
10.1080/07391102.2006.10507094
发表时间：
2006-08-01
影响因子：
4.4
作者：
Avihoo, Assaf;Barash, Danny
通讯作者：
Barash, Danny
影响因子：
3
作者：
Haynes, T;Knisley, D;Seier, E;Zou, Y
通讯作者：
Zou, Y
影响因子：
14.9
作者：
Griffiths-Jones S;Moxon S;Marshall M;Khanna A;Eddy SR;Bateman A
通讯作者：
Bateman A
影响因子：
3
作者：
Cannone JJ;Subramanian S;Schnare MN;Collett JR;D'Souza LM;Du Y;Feng B;Lin N;Madabusi LV;Müller KM;Pande N;Shang Z;Yu N;Gutell RR
通讯作者：
Gutell RR