History
The WGCNA method was developed by Steve Horvath, a professor ofComparison between weighted and unweighted correlation networks
A weighted correlation network can be interpreted as special case of aMethod
First, one defines a gene co-expressionApplications
WGCNA has been widely used for analyzing gene expression data (i.e. transcriptional data), e.g. to find intramodular hub genes. Such as, WGCNA study reveals novel transcription factors are associated with Bisphenol A (BPA) dose-response. It is often used as data reduction step in systems genetic applications where modules are represented by "module eigengenes" e.g. Module eigengenes can be used to correlate modules with clinical traits. Eigengene networks are coexpression networks between module eigengenes (i.e. networks whose nodes are modules) . WGCNA is widely used in neuroscientific applications, e.g. and for analyzing genomic data including microarray data, single cell RNA-Seq data DNA methylation data, miRNA data, peptide counts and microbiota data (16S rRNA gene sequencing). Other applications include brain imaging data, e.g.R software package
The WGCNA R software package provides functions for carrying out all aspects of weighted network analysis (module construction, hub gene selection, module preservation statistics, differential network analysis, network statistics). The WGCNA package is available from the Comprehensive R Archive Network (CRAN), the standard repository for R add-on packages.References
{{reflist, 2, refs= {{cite journal , last1=Chen , first1=Y , last2=Zhu , first2=J , last3=Lum , first3=PY , last4=Yang , first4=X , last5=Pinto , first5=S , last6=MacNeil , first6=DJ , last7=Zhang , first7=C , last8=Lamb , first8=J , last9=Edwards , first9=S , last10=Sieberts , first10=SK , last11=Leonardson , first11=A , last12=Castellini , first12=LW , last13=Wang , first13=S , last14=Champy , first14=MF , last15=Zhang , first15=B , last16=Emilsson , first16=V , last17=Doss , first17=S , last18=Ghazalpour , first18=A , last19=Horvath , first19=S , last20=Drake , first20=TA , last21=Lusis , first21=AJ , last22=Schadt , first22=EE , title=Variations in DNA elucidate molecular networks that cause disease , journal=Nature , date=27 March 2008 , volume=452 , issue=7186 , pages=429–35 , doi=10.1038/nature06757 , pmid=18344982, name-list-style=vanc, pmc=2841398 , bibcode=2008Natur.452..429C {{cite journal , last1=Dong , first1=J , last2=Horvath , first2=S , title=Understanding network concepts in modules , journal=BMC Systems Biology , date=4 June 2007 , volume=1 , pages=24 , doi=10.1186/1752-0509-1-24 , pmid=17547772, pmc=3238286 , name-list-style=vanc {{cite journal , last1=Foroushani , first1=Amir , last2=Agrahari , first2=Rupesh , last3=Docking , first3=Roderick , last4=Chang , first4=Linda , last5=Duns , first5=Gerben , last6=Hudoba , first6=Monika , last7=Karsan , first7=Aly , last8=Zare , first8=Habil , title=Large-scale gene network analysis reveals the significance of extracellular matrix pathway and homeobox genes in acute myeloid leukemia: an introduction to the Pigengene package and its applications , journal=BMC Medical Genomics , date=16 March 2017 , volume=10 , issue=1 , pages=16 , doi=10.1186/s12920-017-0253-6, pmid=28298217 , pmc=5353782 , name-list-style=vanc {{cite journal , last1=Hawrylycz , first1=MJ , last2=Lein , first2=ES , last3=Guillozet-Bongaarts , first3=AL , last4=Shen , first4=EH , last5=Ng , first5=L , last6=Miller , first6=JA , last7=van de Lagemaat , first7=LN , last8=Smith , first8=KA , last9=Ebbert , first9=A , last10=Riley , first10=ZL , last11=Abajian , first11=C , last12=Beckmann , first12=CF , last13=Bernard , first13=A , last14=Bertagnolli , first14=D , last15=Boe , first15=AF , last16=Cartagena , first16=PM , last17=Chakravarty , first17=MM , last18=Chapin , first18=M , last19=Chong , first19=J , last20=Dalley , first20=RA , last21=David Daly , first21=B , last22=Dang , first22=C , last23=Datta , first23=S , last24=Dee , first24=N , last25=Dolbeare , first25=TA , last26=Faber , first26=V , last27=Feng , first27=D , last28=Fowler , first28=DR , last29=Goldy , first29=J , last30=Gregor , first30=BW , last31=Haradon , first31=Z , last32=Haynor , first32=DR , last33=Hohmann , first33=JG , last34=Horvath , first34=S , last35=Howard , first35=RE , last36=Jeromin , first36=A , last37=Jochim , first37=JM , last38=Kinnunen , first38=M , last39=Lau , first39=C , last40=Lazarz , first40=ET , last41=Lee , first41=C , last42=Lemon , first42=TA , last43=Li , first43=L , last44=Li , first44=Y , last45=Morris , first45=JA , last46=Overly , first46=CC , last47=Parker , first47=PD , last48=Parry , first48=SE , last49=Reding , first49=M , last50=Royall , first50=JJ , last51=Schulkin , first51=J , last52=Sequeira , first52=PA , last53=Slaughterbeck , first53=CR , last54=Smith , first54=SC , last55=Sodt , first55=AJ , last56=Sunkin , first56=SM , last57=Swanson , first57=BE , last58=Vawter , first58=MP , last59=Williams , first59=D , last60=Wohnoutka , first60=P , last61=Zielke , first61=HR , last62=Geschwind , first62=DH , last63=Hof , first63=PR , last64=Smith , first64=SM , last65=Koch , first65=C , last66=Grant , first66=SGN , last67=Jones , first67=AR , title=An anatomically comprehensive atlas of the adult human brain transcriptome , journal=Nature , date=20 September 2012 , volume=489 , issue=7416 , pages=391–399 , doi=10.1038/nature11405 , pmid=22996553, pmc=4243026 , name-list-style=vanc, bibcode=2012Natur.489..391H {{cite journal , last1=Horvath , first1=S , last2=Zhang , first2=B , last3=Carlson , first3=M , last4=Lu , first4=KV , last5=Zhu , first5=S , last6=Felciano , first6=RM , last7=Laurance , first7=MF , last8=Zhao , first8=W , last9=Shu , first9=Q , last10=Lee , first10=Y , last11=Scheck , first11=AC , last12=Liau , first12=LM , last13=Wu , first13=H , last14=Geschwind , first14=DH , last15=Febbo , first15=PG , last16=Kornblum , first16=HI , last17=Cloughesy , first17=TF , last18=Nelson , first18=SF , last19=Mischel , first19=PS , authorlink17=Timothy Cloughesy , year=2006 , title=Analysis of Oncogenic Signaling Networks in Glioblastoma Identifies ASPM as a Novel Molecular Target , journal=PNAS , volume=103 , issue=46 , pages=17402–17407 , doi=10.1073/pnas.0608396103 , pmid=17090670 , pmc=1635024 , name-list-style=vanc, bibcode=2006PNAS..10317402H , doi-access=free {{cite journal , last1=Horvath , first1=S , last2=Dong , first2=J , year=2008 , title=Geometric Interpretation of Gene Coexpression Network Analysis , journal=PLOS Computational Biology , volume=4 , issue=8 , page=e1000117 , pmid=18704157 , doi=10.1371/journal.pcbi.1000117 , pmc=2446438, name-list-style=vanc, bibcode=2008PLSCB...4E0117H {{cite book , last1=Horvath , first1=Steve , title=Weighted Network Analysis: Application in Genomics and Systems Biology , date=2011 , publisher=Springer , location=New York, NY , isbn=978-1-4419-8818-8 , name-list-style=vanc {{cite journal , last1=Horvath , first1=S , last2=Zhang , first2=Y , last3=Langfelder , first3=P , last4=Kahn , first4=RS , last5=Boks , first5=MP , last6=van Eijk , first6=K , last7=van den Berg , first7=LH , last8=Ophoff , first8=RA , title=Aging effects on DNA methylation modules in human brain and blood tissue , journal=Genome Biology , date=3 October 2012 , volume=13 , issue=10 , pages=R97 , doi=10.1186/gb-2012-13-10-r97 , pmid=23034122, pmc=4053733 , name-list-style=vanc {{cite journal , last1=Langfelder , first1=P , last2=Zhang , first2=B , last3=Horvath , first3=S , year=2007 , title=Defining clusters from a hierarchical cluster tree: the Dynamic Tree Cut library for R , url= https://semanticscholar.org/paper/20d16d229ed5fddcb9ac1c3a7925582c286d3927, journal=Bioinformatics , volume=24 , issue= 5, pages=719–20 , pmid=18024473 , doi=10.1093/bioinformatics/btm563, s2cid=1095190 , name-list-style=vanc {{cite journal , last1=Langfelder , first1=P , last2=Horvath , first2=S , year=2007 , title=Eigengene networks for studying the relationships between co-expression modules , journal=BMC Systems Biology , volume=2007 , issue=1 , page=54 , pmid=18031580 , doi=10.1186/1752-0509-1-54 , pmc=2267703, name-list-style=vanc {{cite journal , last1=Langfelder , first1=P , last2=Horvath , first2=S , title=WGCNA: an R package for weighted correlation network analysis , journal=BMC Bioinformatics , date=29 December 2008 , volume=9 , pages=559 , doi=10.1186/1471-2105-9-559 , pmid=19114008 , pmc=2631488, name-list-style=vanc {{cite journal , last1=Langfelder , first1=P , last2=Luo , first2=R , last3=Oldham , first3=MC , last4=Horvath , first4=S , title=Is my network module preserved and reproducible? , journal=PLOS Computational Biology , date=20 January 2011 , volume=7 , issue=1 , pages=e1001057 , doi=10.1371/journal.pcbi.1001057 , pmid=21283776, pmc=3024255 , name-list-style=vanc, bibcode=2011PLSCB...7E1057L {{cite journal , last1=Langfelder , first1=Peter , last2=Mischel , first2=Paul S. , last3=Horvath , first3=Steve , last4=Ravasi , first4=Timothy , title=When Is Hub Gene Selection Better than Standard Meta-Analysis? , journal=PLOS ONE , date=17 April 2013 , volume=8 , issue=4 , pages=e61505 , doi=10.1371/journal.pone.0061505, pmid=23613865 , pmc=3629234 , name-list-style=vanc, bibcode=2013PLoSO...861505L , doi-access=free {{cite journal , last1=Mumford , first1=JA , last2=Horvath , first2=S , last3=Oldham , first3=MC , last4=Langfelder , first4=P , last5=Geschwind , first5=DH , last6=Poldrack , first6=RA , title=Detecting network modules in fMRI time series: a weighted network analysis approach , journal=NeuroImage , date=1 October 2010 , volume=52 , issue=4 , pages=1465–76 , doi=10.1016/j.neuroimage.2010.05.047 , pmid=20553896, name-list-style=vanc, pmc=3632300 {{cite journal , last1=Oldham , first1=MC , last2=Langfelder , first2=P , last3=Horvath , first3=S , title=Network methods for describing sample relationships in genomic datasets: application to Huntington's disease , journal=BMC Systems Biology , date=12 June 2012 , volume=6 , pages=63 , doi=10.1186/1752-0509-6-63 , pmid=22691535, pmc=3441531 , name-list-style=vanc {{cite journal , last1=Plaisier , first1=Christopher L. , last2=Horvath , first2=Steve , last3=Huertas-Vazquez , first3=Adriana , last4=Cruz-Bautista , first4=Ivette , last5=Herrera , first5=Miguel F. , last6=Tusie-Luna , first6=Teresa , last7=Aguilar-Salinas , first7=Carlos , last8=Pajukanta , first8=Päivi , last9=Storey , first9=John D. , title=A Systems Genetics Approach Implicates USF1, FADS3, and Other Causal Candidate Genes for Familial Combined Hyperlipidemia , journal=PLOS Genetics , date=11 September 2009 , volume=5 , issue=9 , pages=e1000642 , doi=10.1371/journal.pgen.1000642, pmid=19750004 , pmc=2730565 , name-list-style=vanc {{cite journal , last1=Ranola , first1=JM , last2=Langfelder , first2=P , last3=Lange , first3=K , last4=Horvath , first4=S , title=Cluster and propensity based approximation of a network , journal=BMC Systems Biology , date=14 March 2013 , volume=7 , pages=21 , doi=10.1186/1752-0509-7-21 , pmid=23497424, pmc=3663730 , name-list-style=vanc {{cite journal , last1=Ravasz , first1=E , last2=Somera , first2=AL , last3=Mongru , first3=DA , last4=Oltvai , first4=ZN , last5=Barabasi , first5=AL , year=2002 , title=Hierarchical organization of modularity in metabolic networks , journal=Science , volume=297 , issue=5586 , pages=1551–1555 , doi=10.1126/science.1073374 , pmid=12202830 , arxiv=cond-mat/0209244 , name-list-style=vanc, bibcode=2002Sci...297.1551R , s2cid=14452443 {{cite journal , last1=Shirasaki , first1=DI , last2=Greiner , first2=ER , last3=Al-Ramahi , first3=I , last4=Gray , first4=M , last5=Boontheung , first5=P , last6=Geschwind , first6=DH , last7=Botas , first7=J , last8=Coppola , first8=G , last9=Horvath , first9=S , last10=Loo , first10=JA , last11=Yang , first11=XW , title=Network organization of the huntingtin proteomic interactome in mammalian brain , journal=Neuron , date=12 July 2012 , volume=75 , issue=1 , pages=41–57 , doi=10.1016/j.neuron.2012.05.024 , pmid=22794259, pmc=3432264 , name-list-style=vanc {{cite Q , Q21559533 {{cite journal , last1=Voineagu , first1=I , last2=Wang , first2=X , last3=Johnston , first3=P , last4=Lowe , first4=JK , last5=Tian , first5=Y , last6=Horvath , first6=S , last7=Mill , first7=J , last8=Cantor , first8=RM , last9=Blencowe , first9=BJ , last10=Geschwind , first10=DH , title=Transcriptomic analysis of autistic brain reveals convergent molecular pathology , journal=Nature , date=25 May 2011 , volume=474 , issue=7351 , pages=380–4 , doi=10.1038/nature10110 , pmid=21614001, pmc=3607626 , name-list-style=vanc {{cite journal , last1=Xue , first1=Z , last2=Huang , first2=K , last3=Cai , first3=C , last4=Cai , first4=L , last5=Jiang , first5=CY , last6=Feng , first6=Y , last7=Liu , first7=Z , last8=Zeng , first8=Q , last9=Cheng , first9=L , last10=Sun , first10=YE , last11=Liu , first11=JY , last12=Horvath , first12=S , last13=Fan , first13=G , title=Genetic programs in human and mouse early embryos revealed by single-cell RNA sequencing , journal=Nature , date=29 August 2013 , volume=500 , issue=7464 , pages=593–7 , doi=10.1038/nature12364 , pmid=23892778, pmc=4950944 , name-list-style=vanc, bibcode=2013Natur.500..593X {{cite journal , last1=Yip , first1=AM , last2=Horvath , first2=S , title=Gene network interconnectedness and the generalized topological overlap measure , url= , journal=BMC Bioinformatics , date=24 January 2007 , volume=8 , pages=22 , doi=10.1186/1471-2105-8-22 , pmid=17250769, pmc=1797055 , name-list-style=vanc {{cite journal , last1=Zhang , first1=B , last2=Horvath , first2=S , title=A general framework for weighted gene co-expression network analysis , journal=Statistical Applications in Genetics and Molecular Biology , date=2005 , volume=4 , pages=17 , doi=10.2202/1544-6115.1128 , pmid=16646834 , url=http://dibernardo.tigem.it/files/papers/2008/zhangbin-statappsgeneticsmolbio.pdf, name-list-style=vanc, citeseerx=10.1.1.471.9599 , s2cid=7756201 Bioinformatics Data mining