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HarshavardhanKhare
Biocrystallographylab. Sr.No.08071
Contents
Aim
Complexmolecule
Abstraction
Aim(contd...)
Applicationsandexpectedendresults
Introduction
ElementsofProteinProteinInteraction(PPI) Network
Nodes:Proteinmolecules Edges:Interactions/relationsbetweentwoproteins
Directededges Undirectededges
Abstractionofnodesandedges
Allphysicalandchemicalpropertiesarenot considered.
SchematicrepresentationofPPI network
_________________________________________________
YeastPPInetworkrepresentation
PropertiesofPPInetworks
Powerlawdegreedistribution
P(k)k
Where,kdegreeofnodeandconstant thatdependsuponthenetwork.
PropertiesofPPInetworks(contd...)
Smallworldproperty
Robustness
PropertiesofPPInetworks(contd...)
Herarchicalmodel
Largeclusteringcoefficient
Ci=(Numberofedgespresentinneighbourhoodofnodei)/(Numberof maximumpossibleedgesintheneighbourhoodofnodei)
Thisindicateshowmanynodesintheneighbourhoodof nodeiareconnectedtoeachother.
MethodsofanalysingPPInetworks
Withinnetworkanalysis
Detectingmodules(usuallytheyarefunctionally important)inanetwork
Methods(contd...)
DifinitionofmodulebyRidicchietal[2]
ForasubgraphV G, Strongmoduledefinition: Weakmoduledefinition:
k iin (V ) > kiout (V ) i V
k
iV
in i
(V ) > k iout (V )
iV
Disadvantage:Singlenodecannotbesharedbymorethanone modules.
AlgorithmbyGergelyPallaetal[3]
Methods(contd...)
Methods(contd...)
Betweennetworkanalysis
Comparisonoftwoormorenetworks
Graphinvarientsasdistinguishingcriteria
Methods(contd...)
Mywork:Algorithmbasedonprincpalcomponent analysis
Methods(contd...)
Findouteigenvaluesandeigenvectorsofthismatrix. Theeigenvectorcorrespondingtomaximumeigenvalue iscalledfirstprincipalcomponent(PC1). Itisthevectoralongwhichthevarianceismaximum. Thisimpliesmaximuminformation. PC1softwosuchnetworkswithsamenumberofnodes canbecomparedbasedondifferencesinlengthsor anglebetweenthem. Ifpossible,themeasuresofinteractionotherthanthe simpletopologicaldistancecanbeused.
Applications
Proteinfunctionpredictionbasedonitsinteractionswithother proteins. Predictionofmetabolicpathwayswhererealexperimentsare diffiult. Predictionofpresenceofnewproteinsbycomparingcomplete networkwithanincompleteone. Todiscovernewbiochemicalpathwaysorreactionsandthe conditionsinwhichtheycanoccur. Predictionofdrugtargetsandpossiblesideeffects. Understandingevolutionaryrelationshipbetweendifferent organismsbasedonhowtheirmetabolismworks.
References
1. 'Detectionoffunctionalmodulesfromproteininteractionnetworks,Proteins 54(1):4957,2004',PereiraLealetal 2. 'Definingandidentifyingcommunitiesinnetworks',RadicchiF,CastellanoC, CecconiF,LoretoV,ParisiD;(2004)ProcNatlAcadSciUSA101:2658 2663 3. 'Uncoveringtheoverlappingcommunitystructureofcomplexnetworksin natureandsociety',GergelyPalla,ImreDerenyi,IllesFarkas1&Tamas Vicsek1;Vol435|9June2005|doi:10.1038/nature03607 4. 'Interactiongenerality,ameasurementtoassessthereliabilityofaprotein proteininteraction',Saitoetal.,NAR,30:11631168,2002
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