IHB OpenIR  > 水生生物分子与细胞生物学研究中心  > 期刊论文
Gene Network Landscape of the Ciliate Tetrahymena thermophila
Xiong, Jie; Yuan, Dongxia; Fillingham, Jeffrey S.; Garg, Jyoti; Lu, Xingyi; Chang, Yue; Liu, Yifan; Fu, Chengjie; Pearlman, Ronald E.; Miao, Wei; Xiong, J (reprint author), Chinese Acad Sci, Key Lab Aquat Biodivers & Conservat, Inst Hydrobiol, Wuhan, Peoples R China; miaowei530@yeah.net
2011
Source PublicationPLOS ONE
ISSN1932-6203
Volume6Issue:5Pages:e20124
AbstractBackground: Genome-wide expression data of gene microarrays can be used to infer gene networks. At a cellular level, a gene network provides a picture of the modules in which genes are densely connected, and of the hub genes, which are highly connected with other genes. A gene network is useful to identify the genes involved in the same pathway, in a protein complex or that are co-regulated. In this study, we used different methods to find gene networks in the ciliate Tetrahymena thermophila, and describe some important properties of this network, such as modules and hubs. Methodology/Principal Findings: Using 67 single channel microarrays, we constructed the Tetrahymena gene network (TGN) using three methods: the Pearson correlation coefficient (PCC), the Spearman correlation coefficient (SCC) and the context likelihood of relatedness (CLR) algorithm. The accuracy and coverage of the three networks were evaluated using four conserved protein complexes in yeast. The CLR network with a Z-score threshold 3.49 was determined to be the most robust. The TGN was partitioned, and 55 modules were found. In addition, analysis of the arbitrarily determined 1200 hubs showed that these hubs could be sorted into six groups according to their expression profiles. We also investigated human disease orthologs in Tetrahymena that are missing in yeast and provide evidence indicating that some of these are involved in the same process in Tetrahymena as in human. Conclusions/Significance: This study constructed a Tetrahymena gene network, provided new insights to the properties of this biological network, and presents an important resource to study Tetrahymena genes at the pathway level.
KeywordRetinoblastoma Protein Family Dna Elimination Genome Rearrangement Biological Networks Cell-cycle Coexpression Network Functional Modules Microarray Data Human Cdc2 Small Rnas
Department[Xiong, Jie; Yuan, Dongxia; Lu, Xingyi; Chang, Yue; Fu, Chengjie; Miao, Wei] Chinese Acad Sci, Key Lab Aquat Biodivers & Conservat, Inst Hydrobiol, Wuhan, Peoples R China; [Xiong, Jie; Lu, Xingyi; Chang, Yue] Chinese Acad Sci, Grad Sch, Beijing, Peoples R China; [Yuan, Dongxia] Chinese Acad Sci, State Key Lab Freshwater Ecol & Biotechnol, Inst Hydrobiol, Wuhan, Peoples R China; [Fillingham, Jeffrey S.] Ryerson Univ, Dept Biol & Chem, Toronto, ON, Canada; [Garg, Jyoti; Pearlman, Ronald E.] York Univ, Ctr Res Mass Spectrometry, Toronto, ON M3J 2R7, Canada; [Garg, Jyoti; Pearlman, Ronald E.] York Univ, Dept Biol, Toronto, ON M3J 2R7, Canada; [Liu, Yifan] Univ Michigan, Sch Med, Dept Pathol, Ann Arbor, MI USA
Subject AreaLife Sciences & Biomedicine - Other Topics
Funding OrganizationNational Natural Science Foundation of China[31071993]; CAS[KSCX2-YW-G-072]; Canadian Institutes of Health Research[MOP 97799]; Ryerson University; National Institutes of Health[GM087343] ; National Natural Science Foundation of China[31071993]; CAS[KSCX2-YW-G-072]; Canadian Institutes of Health Research[MOP 97799]; Ryerson University; National Institutes of Health[GM087343] ; National Natural Science Foundation of China[31071993]; CAS[KSCX2-YW-G-072]; Canadian Institutes of Health Research[MOP 97799]; Ryerson University; National Institutes of Health[GM087343] ; National Natural Science Foundation of China[31071993]; CAS[KSCX2-YW-G-072]; Canadian Institutes of Health Research[MOP 97799]; Ryerson University; National Institutes of Health[GM087343]
Indexed BySCI
Language英语
WOS IDWOS:000291052200034
Funding OrganizationNational Natural Science Foundation of China[31071993]; CAS[KSCX2-YW-G-072]; Canadian Institutes of Health Research[MOP 97799]; Ryerson University; National Institutes of Health[GM087343] ; National Natural Science Foundation of China[31071993]; CAS[KSCX2-YW-G-072]; Canadian Institutes of Health Research[MOP 97799]; Ryerson University; National Institutes of Health[GM087343] ; National Natural Science Foundation of China[31071993]; CAS[KSCX2-YW-G-072]; Canadian Institutes of Health Research[MOP 97799]; Ryerson University; National Institutes of Health[GM087343] ; National Natural Science Foundation of China[31071993]; CAS[KSCX2-YW-G-072]; Canadian Institutes of Health Research[MOP 97799]; Ryerson University; National Institutes of Health[GM087343]
Citation statistics
Cited Times:17[WOS]   [WOS Record]     [Related Records in WOS]
Document Type期刊论文
Identifierhttp://ir.ihb.ac.cn/handle/342005/16473
Collection水生生物分子与细胞生物学研究中心_期刊论文
Corresponding AuthorXiong, J (reprint author), Chinese Acad Sci, Key Lab Aquat Biodivers & Conservat, Inst Hydrobiol, Wuhan, Peoples R China; miaowei530@yeah.net
Recommended Citation
GB/T 7714
Xiong, Jie,Yuan, Dongxia,Fillingham, Jeffrey S.,et al. Gene Network Landscape of the Ciliate Tetrahymena thermophila[J]. PLOS ONE,2011,6(5):e20124.
APA Xiong, Jie.,Yuan, Dongxia.,Fillingham, Jeffrey S..,Garg, Jyoti.,Lu, Xingyi.,...&miaowei530@yeah.net.(2011).Gene Network Landscape of the Ciliate Tetrahymena thermophila.PLOS ONE,6(5),e20124.
MLA Xiong, Jie,et al."Gene Network Landscape of the Ciliate Tetrahymena thermophila".PLOS ONE 6.5(2011):e20124.
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