作者
:
宋长新 雷萍 王婷
文章题名
:
英文篇名 : Gene Co-expression Network Analysis Based on WGCNA Algorithm-Theory and Implementation in R Software
标识号
:
ISSN : 1674-568X CN : 45-1369/Q
中文关键词
:
WGCNA算法;基因共表达网络;R软件
英文关键词
:
WGCNA, Gene co-expression network, R software
作者机构
:
青海师范大学计算机学院;深圳市水质检测中心
基金
:
青海省135高层次人才培养基金资助
分类号
:
中图分类 : Q78
引文
:
Aggarwal A.,Guo D.L.,Hoshida Y.,Yuen S.T.,Chu K.M.,So S.,Boussioutas A.,Chen X.,Bowtell D.,Aburatani H.,LeungS.Y.,and Tan P.,2006,Topological and functional discov-ery in a gene coexpression meta-network of gastric cancer,Cancer Res.,66(1):232-241
Barabási A.L.,2009,Scale-free networks:A decade and beyond,Science,325(5939):412-413
Carter S.L.,Brechbühler C.M.,Griffin M.,and Bond A.T.,2004,Gene co-expression network topology provides a frameworkfor molecular characterization of cellular state,Bioinformat-ics,20(14):2242-2250
Chen C.,2011,Evaluation of six batch adjustment methods inexpression microarray data and application of gene co-ex-pression network in schizophrenia,Dissertation for Ph.D.,Fudan University,Supervisor:Jin L.,pp.81-86(陈超,2011,基因表达谱芯片校正批次效应算法的比较及网络分析在精神分裂症研究中的应用,博士学位论文,复旦大学,导师:金立,pp.81-86)
Childs K.L.,Davidson R.M.,and Buell C.R.,2011,Gene coex-pression network analysis as a source of functional annota-tion for rice genes,PLoS One,6(7):e22196
Dewey F.E.,Perez M.V.,Wheeler M.T.,Watt C.,Spin J.,Langfelder P.,Horvath S.,Hannenhalli S.,Cappola T.P.,and Ashley E.A.,2010,Gene coexpression network topolo-gy of cardiac development,hypertrophy,and failure,Circ.Cardiovasc.Genet.,4(1):26-35
Dong J.,and Horvath S.,2007,Understanding network conceptsin modules,BMC Syst.Biol.,1:24
Farber C.R.,2010,Identification of a gene module associatedwith BMD through the integration of network analysis andgenome-wide association data,J.Bone Miner.Res.,25(11):2359-2367
Ficklin S.P.,and Feltus F.A.,2011,Gene coexpression networkalignment and conservation of gene modules between two grassspecies:Maizeandrice,PlantPhysiol.,156(3):1244-1256
Horvath S.,Zhang B.,Carlson M.,Lu K.V.,Zhu S.,Felciano R.M.,Laurance M.F.,Zhao W.,Qi S.,Chen Z.,Lee Y.,Scheck A.C.,Liau L.M.,Wu H.,Geschwind D.H.,Febbo P.G.,Kornblum H.I.,Cloughesy T.F.,Nelson S.F.,and Mis-chel P.S.,2006,Analysis of oncogenic signaling networks inglioblastoma identifies ASPM as a novel molecular target,PNAS,103(46):17402-17407
Kiel D.P.,Demissie S.,Dupuis J.,Lunetta K.L.,Murabito J.M.,and Karasik D.,2007,Genome-wide association with bonemass and geometry in the framingham heart study,BMCMed.Genet.,8(Suppl1):S14
Langfelder P.,and Horvath S.,2008,WGCNA:An R package forweighted correlation network analysis,BMC Bioinformat-ics,9:559
Langfelder P.,Zhang B.,and Horvath S.,2008,Defining clustersfrom a hierarchical cluster tree:The dynamic tree cut pack-age for R,Bioinformatics,24(5):719-720
Miller J.A.,Horvath S.,and Geschwind D.H.,2010,Divergenceof human and mouse brain transcriptome highlights Alzhe-imer disease pathways,PNAS,107(28):12698-12703
Nayak R.R.,Kearns M.,Spielman R.S.,and Cheung V.G.,2009,Coexpression network based on natural variation in humangene expression reveals gene interactions and functions,Genome Res.,19(11):1953-1962
Plaisier C.L.,Horvath S.,Huertas-Vazquez A.,Cruz-Bautista I.,Herrera M.F.,Tusie-Luna T.,Aguilar-Salinas C.,and Pa-jukanta P.,2009,A systems genetics approach implicatesUSF1,FADS3,and other causal candidate genes for familialcombined hyperlipidemia,PLoS Genet.,5(9):e1000642
Ravasz E.,Somera A.L.,Mongru D.A.,Oltvai Z.N.,and BarabásiA.L.,2002,Hierarchical organization of modularity inmetabolic networks,Science,297(5586):1551-1555
Styrkarsdottir U.,Halldorsson B.V.,Gretarsdottir S.,Gudbjarts-son D.F.,Walters G.,Ingvarsson T.,Jonsdottir T.,Saemu-ndsdottir J.,Center J.R.,Nguyen T.V.,Bagger Y.,GulcherJ.R.,Eisman J.A.,Christiansen C.,Sigurdsson G.,Kong A.,Thorsteinsdottir U.,and Stefansson K.,2008,Multiple ge-netic loci for bone mineral density and fractures,N.Engl.J.Med.,358(22):2355-2365
Voineagu I.,Wang X.,Johnston P.,Lowe J.K.,Tian Y.,Horvath S.,Mill J.,Cantor R.M.,Blencowe B.J.,and Geschwind D.H.,2011,Transcriptomic analysis of autistic brain reveals con-vergent molecular pathology,Nature,474(7351):380-384
Zhang B.,and Horvath S.,2005,A general framework forweighted gene co-expression network analysis,Stat.Appl.Genet.Mol.Biol.,4:Article17
Zheng X.,Liu T.,Yang Z.,and Wang J.,2011,Large cliques inArabidopsisgene coexpression network and motif discovery,J.Plant Physiol.,168(6):611-618
来源
:
基因组学与应用生物学, Genomics and Applied Biology,2013,01
刊名
:
基因组学与应用生物学 Genomics and Applied Biology
年
:
2013
期
:
01
页
:
143-149
页数
:
7
印刷页码
:
135-141
更新日期
:
2013-04-18