Download Gene co-expression networks

6/07/16
Weightedgenecoexpressionnetwork
analysis(WGCNA)prac;cal
Integra;veGenomicsmodule
MichaelInouye
CentreforSystemsGenomics
UniversityofMelbourne,Australia
SummerIns@tuteinSta@s@calGene@cs2016
SeaBle,USA
@minouye271
inouyelab.org
Geneco-expressionnetworks
•  Weighted,undirected
completegenenetwork
–  Nodes:genes/probes
–  Edges:|cor(node_i,node_j)|γ
•  Scale-freeassump@onand[0,1]
•  Iden;fysubnets(modules/
clusters)
–  Typicallysubnetsrepresent
knownbiologicalpathways
–  Variousmethodsandtoolsfor
clustering
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Whatwe’redoingtoday
•  Datamanagementandfiltering
•  Networkconstruc@on
•  Moduledetec@on
•  Moduleassocia@onanalysis
GeHngstarted
(ifyouhaven’talreadydoneso)
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What’sitdoing?
•  CalculatePearsoncorrela@oncoefficients
betweenallpairsofgenes
•  Useapowertransformtosa@sfyscale-free
topologycriteria(selectso]powerthreshold)
•  Inferanetworkwhere
–  Nodes:Genes
–  Edges:Pearsoncorrela@onsraisedtotheselected
power
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What’sitdoing?
•  Goal:Getthemostcoherentgenesubnetworksaspossible
•  Insteadofusingthecorrela@on-basededges,WGCNAis
calcula@ngadistancemeasurecalledtopologicalsimilarity
(TOM):
Yip&Horvath,BMCBioinf2007
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What’sitdoing?
•  HierarchicalclusteringofTOMmatrix
•  Movethroughthedendrogramwitha
dynamiccufngalgorithm
Yip&Horvath,BMCBioinf2007
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Phenotypeassocia;onanalysis
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SpecialthankstoScoLRitchie
Networkinferenceadaptedfromhisscript
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