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	Identifying modules of coexpressed transcript units and their organization of saccharopolyspora erythraea from time series gene expression profiles
	Chang, Xiao1,2,3; Liu, Shuai4; Yu, Yong-Tao2; Li, Yi-Xue1,2; Li, Yuan-Yuan1,2
刊名	Plos one
	2010-08-12
卷号	5期号:8页码:8
ISSN号	1932-6203
DOI	10.1371/journal.pone.0012126
通讯作者	Chang, xiao()
英文摘要	Background: the saccharopolyspora erythraea genome sequence was released in 2007. in order to look at the gene regulations at whole transcriptome level, an expression microarray was specifically designed on the s. erythraea strain nrrl 2338 genome sequence. based on these data, we set out to investigate the potential transcriptional regulatory networks and their organization. methodology/principal findings: in view of the hierarchical structure of bacterial transcriptional regulation, we constructed a hierarchical coexpression network at whole transcriptome level. a total of 27 modules were identified from 1255 differentially expressed transcript units (tus) across time course, which were further classified in to four groups. functional enrichment analysis indicated the biological significance of our hierarchical network. it was indicated that primary metabolism is activated in the first rapid growth phase (phase a), and secondary metabolism is induced when the growth is slowed down (phase b). among the 27 modules, two are highly correlated to erythromycin production. one contains all genes in the erythromycin-biosynthetic (ery) gene cluster and the other seems to be associated with erythromycin production by sharing common intermediate metabolites. non-concomitant correlation between production and expression regulation was observed. especially, by calculating the partial correlation coefficients and building the network based on gaussian graphical model, intrinsic associations between modules were found, and the association between those two erythromycin production-correlated modules was included as expected. conclusions: this work created a hierarchical model clustering transcriptome data into coordinated modules, and modules into groups across the time course, giving insight into the concerted transcriptional regulations especially the regulation corresponding to erythromycin production of s. erythraea. this strategy may be extendable to studies on other prokaryotic microorganisms.
WOS关键词	REGULATORY NETWORKS ; ERYTHROMYCIN ; ALGORITHM ; OPERONS
WOS研究方向	Science & Technology - Other Topics
WOS类目	Multidisciplinary Sciences
语种	英语
出版者	PUBLIC LIBRARY SCIENCE
WOS记录号	WOS:000280859700018
内容类型	期刊论文
URI标识	http://www.corc.org.cn/handle/1471x/2408746
专题	中国科学院大学
通讯作者	Chang, Xiao
作者单位	1.Chinese Acad Sci, Shanghai Inst Biol Sci, Bioinformat Ctr, Key Lab Syst Biol, Shanghai, Peoples R China 2.Shanghai Ctr Bioinformat Technol, Shanghai, Peoples R China 3.Chinese Acad Sci, Grad Sch, Beijing, Peoples R China 4.Test Ctr Agr Qual Jinan, Jinan, Peoples R China
推荐引用方式 GB/T 7714	Chang, Xiao,Liu, Shuai,Yu, Yong-Tao,et al. Identifying modules of coexpressed transcript units and their organization of saccharopolyspora erythraea from time series gene expression profiles[J]. Plos one,2010,5(8):8.
APA	Chang, Xiao,Liu, Shuai,Yu, Yong-Tao,Li, Yi-Xue,&Li, Yuan-Yuan.(2010).Identifying modules of coexpressed transcript units and their organization of saccharopolyspora erythraea from time series gene expression profiles.Plos one,5(8),8.
MLA	Chang, Xiao,et al."Identifying modules of coexpressed transcript units and their organization of saccharopolyspora erythraea from time series gene expression profiles".Plos one 5.8(2010):8.

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