Corbi: a new R package for biological network alignment and querying

doi:10.1186/1752-0509-7-S2-S6

CSpace > 应用数学研究所

	Corbi: a new R package for biological network alignment and querying
	Huang,Qiang 1,2; Wu,Ling-Yun1,2 ; Zhang,Xiang-Sun1,2
	2013-10-14
发表期刊	BMC Systems Biology
ISSN	1752-0509
卷号	7 期号:Suppl 2
摘要	AbstractIn the last decade, plenty of biological networks are built from the large scale experimental data produced by the rapidly developing high-throughput techniques as well as literature and other sources. But the huge amount of network data have not been fully utilized due to the limited biological network analysis tools. As a basic and essential bioinformatics method, biological network alignment and querying have been applied in many fields such as predicting new protein-protein interactions (PPI). Although many algorithms were published, the network alignment and querying problems are not solved satisfactorily. In this paper, we extended CNetQ, a novel network querying method based on the conditional random fields model, to solve network alignment problem, by adopting an iterative bi-directional mapping strategy. The new method, called CNetA, was compared with other four methods on fifty simulated and three real PPI network alignment instances by using four structural and five biological measures. The computational experiments on the simulated data, which were generated from a biological network evolutionary model to validate the effectiveness of network alignment methods, show that CNetA gets the best accuracy in terms of both nodes and networks. For the real data, larger biological conserved subnetworks and larger connected subnetworks were identified, compared with the structural-dominated methods and the biological-dominated methods, respectively, which suggests that CNetA can better balances the biological and structural similarities. Further, CNetQ and CNetA have been implemented in a new R package Corbi (http://doc.aporc.org/wiki/Corbi), and freely accessible and easy used web services for CNetQ and CNetA have also been constructed based on the R package. The simulated and real datasets used in this paper are available for downloading at http://doc.aporc.org/wiki/CNetA/
DOI	10.1186/1752-0509-7-S2-S6
语种	英语
WOS记录号	BMC:10.1186/1752-0509-7-S2-S6
出版者	BioMed Central
引用统计
文献类型	期刊论文
条目标识符	http://ir.amss.ac.cn/handle/2S8OKBNM/273
专题	应用数学研究所
通讯作者	Wu,Ling-Yun
作者单位	1.CAS; National Center for Mathematics and Interdisciplinary Sciences 2.Academy of Mathematics and Systems Science, CAS; Institute of Applied Mathematics
推荐引用方式 GB/T 7714	Huang,Qiang,Wu,Ling-Yun,Zhang,Xiang-Sun. Corbi: a new R package for biological network alignment and querying[J]. BMC Systems Biology,2013,7(Suppl 2).
APA	Huang,Qiang,Wu,Ling-Yun,&Zhang,Xiang-Sun.(2013).Corbi: a new R package for biological network alignment and querying.BMC Systems Biology,7(Suppl 2).
MLA	Huang,Qiang,et al."Corbi: a new R package for biological network alignment and querying".BMC Systems Biology 7.Suppl 2(2013).