A method to detect gene Co-expression clusters from multiple microarrays

	A method to detect gene Co-expression clusters from multiple microarrays
	Chen Lan 1,3; Wang Shi-Min 1,3; Chen Run-Sheng 1,2
	2008-08-01
发表期刊	PROGRESS IN BIOCHEMISTRY AND BIOPHYSICS
ISSN	1000-3282
卷号	35 期号:8 页码:914-920
摘要	A number of recent studies have focused oil discovering genetic functional or transcriptional modules by integrating information from the rapidly accumulating large-scale microarray expression datasets. Such Studies commonly model each microarray as a co-expression network, and detect the conserved gene co-expression Clusters from these co-expression networks. Currently, the commonly used method is mining conserved co-expression clusters directly from a "summary network", which is obtained by aggregating all the co-expression networks derived from different microarrays. However, this method may generate false conserved clusters, which never occur in any of the original individual co-expression networks. Here a scalable and efficient method were proposed to detect the truly conserved gene co-expression clusters from multiple microarrays. This problem is formulated as mining frequently occurring subgraphs across multiple co-expression networks, and involves three steps: (1) Translating each microarray into co-expression network; (2) Clustering edges which occur in the similar co-expression networks by min-hashing and locality-sensitive hashing techniques to obtain the candidate clusters; (3) Applying graph clustering method to the candidate clusters to detect the conserved co-expressed clusters. This method was applied to yeast microarrays and the results demonstrate that, compared to the previous study, the conserved co-expressed clusters detected by the method were more likely to be functionally homogeneous entities or potential transcriptional modules.
关键词	microarray co-expression network min-hashing locality-sensitive hashing
收录类别	SCI
语种	英语
资助项目	The National Natural Sciences Foundation of China[30630040] ; The National Natural Sciences Foundation of China[30570393] ; The National Natural Sciences Foundation of China[30600729]
WOS研究方向	Biochemistry & Molecular Biology ; Biophysics
WOS类目	Biochemistry & Molecular Biology ; Biophysics
WOS记录号	WOS:000258678400009
出版者	CHINESE ACAD SCIENCES, INST BIOPHYSICS
引用统计	被引频次：2[WOS] [WOS记录] [WOS相关记录]
文献类型	期刊论文
条目标识符	http://119.78.100.204/handle/2XEOYT63/11313
专题	中国科学院计算技术研究所期刊论文_英文
通讯作者	Chen Run-Sheng
作者单位	1.Chinese Acad Sci, Inst Comp Technol, Bioinformat Res Grp, Beijing 100190, Peoples R China 2.Chinese Acad Sci, Inst Biophys, Bioinformat Lab, Beijing 100101, Peoples R China 3.Chinese Acad Sci, Grad Sch, Beijing 100049, Peoples R China
推荐引用方式 GB/T 7714	Chen Lan,Wang Shi-Min,Chen Run-Sheng. A method to detect gene Co-expression clusters from multiple microarrays[J]. PROGRESS IN BIOCHEMISTRY AND BIOPHYSICS,2008,35(8):914-920.
APA	Chen Lan,Wang Shi-Min,&Chen Run-Sheng.(2008).A method to detect gene Co-expression clusters from multiple microarrays.PROGRESS IN BIOCHEMISTRY AND BIOPHYSICS,35(8),914-920.
MLA	Chen Lan,et al."A method to detect gene Co-expression clusters from multiple microarrays".PROGRESS IN BIOCHEMISTRY AND BIOPHYSICS 35.8(2008):914-920.