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
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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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