多类代谢组学中练习10 poplar id.pdfVIP

MVDA-ExercisePOPLAR

OPLSinmulticlassmetabolomics

Background

ThierciseisthestudyofgeneticallymodifiedpoplarplantsbyGC/MSmetabolomics.Two

modificationsareinvestigatedi.e.upregulationanddownregulationwithinthePttPME1gene.This

geneisinvolvedintheproductionofpectinmethylesterase,PME,whichisanenzymethatde-

esterifiesmethylatedgroupswithinpectin.Pectinisbigcomplexpolymerandwillnotbeanalyzedby

thistypeoftechnique.Nevertheless,themetabolicprofilewasofinterestasbothlinesindicated

severalsymptomsofoxidativestressresponse.

Objective

TheobjectiveofthierciseistoshedsomelightonhowOPLSmaybeusedinstate-of-the-artmulti

classMetabolomics.Inparticular,theobjectivesareto:

•demonstratehowtoextractputativebiomarkersfromtheS-plot

•demonstratehowtoprovidestatisticalevidencetoextractedbiomarkers

•demonstratehowtoextractinformationthatisunrelated(orthogonal)tothemodelled

response,y

•demonstratehowtocomparemultipleclassesbytheuseofaSUS-plot

Data

Intotal,thedatasetcontainsN=26observations(plants)andK=80variables(resolvedand

integratedGC/MSprofilesbytheuseofH-MCR[1]).Theobservations(plants)aredividedinthree

groups(“classes”):

•ControlWildtypeplant,10plants“WT”

•PttPME1downregulatedpoplar,L5,7plants“L5”

•PttPME1upregulatedpoplar,9plants“2B”

TheGC/MSdataarethree-waybynaturewithtime,absorbanceandmassdimensions.Inthiample

thethreewaydatahavebeenpre-processedbyHierarchicalMultivariateCurveResolution,H-MCR

[1].H-MCRresolvesthechromaticpr