中国科学院水生生物研究所机构知识库
Advanced  
IHB OpenIR  > 水生生物分子与细胞生物学研究中心  > 期刊论文
学科主题: Life Sciences & Biomedicine - Other Topics
题名: Gene Network Landscape of the Ciliate Tetrahymena thermophila
作者: Xiong, Jie1, 2; Yuan, Dongxia1, 3; Fillingham, Jeffrey S.4; Garg, Jyoti5, 6; Lu, Xingyi1, 2; Chang, Yue1, 2; Liu, Yifan7; Fu, Chengjie1; Pearlman, Ronald E.5, 6; Miao, Wei1
通讯作者: Xiong, J (reprint author), Chinese Acad Sci, Key Lab Aquat Biodivers & Conservat, Inst Hydrobiol, Wuhan, Peoples R China ; miaowei530@yeah.net
关键词: RETINOBLASTOMA PROTEIN FAMILY ; DNA ELIMINATION ; GENOME REARRANGEMENT ; BIOLOGICAL NETWORKS ; CELL-CYCLE ; COEXPRESSION NETWORK ; FUNCTIONAL MODULES ; MICROARRAY DATA ; HUMAN CDC2 ; SMALL RNAS
刊名: PLOS ONE
发表日期: 2011-05-26
DOI: 10.1371/journal.pone.0020124
卷: 6, 期:5, 页:e20124
收录类别: SCI
文章类型: Article
部门归属: [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
WOS标题词: Science & Technology
资助者: 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]
类目[WOS]: Multidisciplinary Sciences
研究领域[WOS]: Science & Technology - Other Topics
摘要: Background: 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.
英文摘要: Background: 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.
关键词[WOS]: RETINOBLASTOMA PROTEIN FAMILY ; DNA ELIMINATION ; GENOME REARRANGEMENT ; BIOLOGICAL NETWORKS ; CELL-CYCLE ; COEXPRESSION NETWORK ; FUNCTIONAL MODULES ; MICROARRAY DATA ; HUMAN CDC2 ; SMALL RNAS
语种: 英语
WOS记录号: WOS:000291052200034
ISSN号: 1932-6203
Citation statistics:
内容类型: 期刊论文
URI标识: http://ir.ihb.ac.cn/handle/342005/16473
Appears in Collections:水生生物分子与细胞生物学研究中心_期刊论文

Files in This Item: Download All
File Name/ File Size Content Type Version Access License
Gene Network Landscape of the Ciliate Tetrahymena thermophila.pdf(447KB)----开放获取--View Download

作者单位: 1.Chinese Acad Sci, Key Lab Aquat Biodivers & Conservat, Inst Hydrobiol, Wuhan, Peoples R China
2.Chinese Acad Sci, Grad Sch, Beijing, Peoples R China
3.Chinese Acad Sci, State Key Lab Freshwater Ecol & Biotechnol, Inst Hydrobiol, Wuhan, Peoples R China
4.Ryerson Univ, Dept Biol & Chem, Toronto, ON, Canada
5.York Univ, Ctr Res Mass Spectrometry, Toronto, ON M3J 2R7, Canada
6.York Univ, Dept Biol, Toronto, ON M3J 2R7, Canada
7.Univ Michigan, Sch Med, Dept Pathol, Ann Arbor, MI USA

Recommended Citation:
Xiong, Jie; Yuan, Dongxia; Fillingham, Jeffrey S.; Garg, Jyoti; Lu, Xingyi; Chang, Yue; Liu, Yifan; Fu, Chengjie; Pearlman, Ronald E.; Miao, Wei.Gene Network Landscape of the Ciliate Tetrahymena thermophila,PLOS ONE,2011,6(5):e20124
Service
Recommend this item
Sava as my favorate item
Show this item's statistics
Export Endnote File
Google Scholar
Similar articles in Google Scholar
[Xiong, Jie]'s Articles
[Yuan, Dongxia]'s Articles
[Fillingham, Jeffrey S.]'s Articles
CSDL cross search
Similar articles in CSDL Cross Search
[Xiong, Jie]‘s Articles
[Yuan, Dongxia]‘s Articles
[Fillingham, Jeffrey S.]‘s Articles
Related Copyright Policies
Null
Social Bookmarking
Add to CiteULike Add to Connotea Add to Del.icio.us Add to Digg Add to Reddit
文件名: Gene Network Landscape of the Ciliate Tetrahymena thermophila.pdf
格式: Adobe PDF
所有评论 (0)
暂无评论
 
评注功能仅针对注册用户开放,请您登录
您对该条目有什么异议,请填写以下表单,管理员会尽快联系您。
内 容:
Email:  *
单位:
验证码:   刷新
您在IR的使用过程中有什么好的想法或者建议可以反馈给我们。
标 题:
 *
内 容:
Email:  *
验证码:   刷新

Items in IR are protected by copyright, with all rights reserved, unless otherwise indicated.

 

 

Valid XHTML 1.0!
Copyright © 2007-2017  中国科学院水生生物研究所 - Feedback
Powered by CSpace