Clustering incorporating shortest paths identifies relevant modules in functional interaction networks

机译：包含最短路径的聚类可识别功能交互网络中的相关模块

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Many biological systems can be modeled as networks. Hence, network analysis is of increasing importance to systems biology. We describe an evolutionary algorithm for selecting clusters of nodes within a large network based upon network topology together with a measure of the relevance of nodes to a set of independently identified genes of interest. We apply the algorithm to a previously published integrated functional network of yeast genes, using a set of query genes derived from a whole genome screen of yeast strains with a mutation in a telomere uncapping gene. We find that the algorithm identifies biologically plausible clusters of genes which are related to the cell cycle, and which contain interactions not previously identified as potentially important. We conclude that the algorithm is valuable for the querying of complex networks, and the generation of biological hypotheses.

机译：许多生物系统可以建模为网络。因此，网络分析对系统生物学的重要性日益增加。我们描述了一种进化算法，用于根据网络拓扑选择大型网络中节点的群集以及节点与一组独立识别的目标基因相关性的度量。我们将算法应用于酵母基因的先前发布的集成功能网络，使用一组查询基因，该查询基因来自端粒解键基因突变的酵母菌株的全基因组筛选。我们发现，该算法可以识别与细胞周期相关的基因的生物学上合理的簇，并且其中包含的相互作用以前并未被确定为潜在重要。我们得出结论，该算法对于复杂网络的查询以及生物学假设的产生都是有价值的。

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来源
《Computational Intelligence in Bioinformatics and Computational Biology, 2009. CIBCB '09》|2009年|228-236|共9页
会议地点 Nashville TN(US);Nashville TN(US)
作者
Hallinan J.; Pocock M.; Addinall S.; Lydall D.A.; Wipat A.;
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Sch. of Comput. Sci., Newcastle Univ., Newcastle upon Tyne;

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biocybernetics; cellular biophysics; evolutionary computation; genomics; microorganisms; molecular biophysics; network theory (graphs); biological systems; biologically plausible gene clusters; cell cycle; complex network querying; evolutionary algorithm; functional interaction network modules; large network; network analysis; network topology; node clustering; node relevance; query gene set; shortest path; systems biology; telomere uncapping gene mutation; yeast gene integrated functional network; yeast strain genome;

机译：生物cybernetics;细胞生物物理学;进化计算;基因组学;微生物;分子生物物理学;网络理论（图）;生物系统;生物学上合理的基因簇;细胞周期;复杂网络查询;进化算法;功能相互作用网络模块;大型网络;网络分析;网络拓扑;节点聚类;节点相关性;查询基因集;最短路径;系统生物学;端粒解封基因突变;酵母基因整合功能网络;酵母菌株基因组;

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专利

1. Identifying functional modules in interaction networks through overlapping Markov clustering [J] . Shih Yu-Keng, Parthasarathy Srinivasan Bioinformatics . 2012,第18期

机译：通过重叠马尔可夫聚类识别交互网络中的功能模块
2. Identifying functional modules in interaction networks through overlapping Markov clustering [J] . Yu-Keng Shih and Srinivasan Parthasarathy* Bioinformatics . 2012,第18期

机译：通过重叠马尔可夫聚类识别交互网络中的功能模块
3. A Markov Clustering Based Link Clustering Method to Identify Overlapping Modules in Protein-Protein Interaction Networks [J] . Wang Yan, Wang Guishen, Meng Di, Current Bioinformatics . 2016,第2期

机译：基于Markov聚类的链接聚类方法识别蛋白质-蛋白质相互作用网络中的重叠模块
4. Clustering Incorporating Shortest Paths Identifies Relevant Modules in Functional Interaction Networks [C] . Jennifer Hallinan, Matthew Pocock, Stephen Addinall, IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology . 2009

机译：包含最短路径的聚类识别功能交互网络中的相关模块
5. FAC-PIN: An efficient and fast agglomerative clustering algorithm for protein interaction networks to predict protein complexes and functional modules. [D] . Rahman, Mohammad Shamsur. 2013

机译：FAC-PIN：一种高效且快速的聚集聚类算法，用于蛋白质相互作用网络来预测蛋白质复合物和功能模块。
6. Identifying functional modules in interaction networks through overlapping Markov clustering [O] . Yu-Keng Shih, Srinivasan Parthasarathy -1

机译：通过重叠马尔可夫聚类识别交互网络中的功能模块
7. Clustering Incorporating Shortest Paths Identifies Relevant Modules in Functional Interaction Networks [O] . Jennifer Hallinan, Matthew Pocock, Stephen Addinall, 2015

机译：包含最短路径的聚类识别功能交互网络中的相关模块

Clustering incorporating shortest paths identifies relevant modules in functional interaction networks

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