Genome Informatics 14 559–560 (2003) 559 PLOC Prediction of Subcellular Location of Protei

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GenomeInformatics14:559–560(2003)559
PLOC:PredictionofSubcellularLocationofProteins
Keun-JoonPark1MinoruKanehisa
2
park-kj@aist.go.jpkanehisa@kuicr.kyoto-u.ac.jp
YutakaAkiyama
1
akiyama@cbrc.jp
1
ComputationalBiologyResearchCenter(CBRC),NationalInstituteofAdvanced

IndustrialScienceandTechnology(AIST),AomiFrontierBldg.17F,2-43Aomi,
Koto-ku,Tokyo135-0064,Japan
2
BioinformaticsCenter,InstituteforChemicalResearch,KyotoUniversity,Uji,Kyoto

611-0011,Japan

Keywords:sequenceanalysis,supportvectormachines,subcellularlocalization
1Introduction

Figure1:ScreenshotofthePLOCandtheexampleofresult.
Tounderstandthefunctionsofvarious
proteins,itwouldbehelpfultoobtain
informationabouttheirsubcellularlo-
cation.Thisisbecausethesubcellular
locationofproteinsiscloselyrelated
totheirfunction.Thus,itwouldbe
worthwhiletodevelopafastcompu-
tationalpredictionmethodtoidentify
protein’ssubcellularlocation.
Inthisresearch,wehavedevel-
opedapredictiontoolnamedPLOC
(ProteinLOCalizationprediction)us-
ingthecompositionsofaminoacids
and(gapped)aminoacidpairsbysup-
portvectormachines[2].
Thispredictionmethodisavailableathttp://www.genome.ad.jp/SIT/ploc.html(Figure1).

2MethodandResults
Weconsidered12subcellularlocationsineukaryoticcells:chloroplast,cytoplasm,cytoskeleton,en-
doplasmicreticulum,extracellularmedium,Golgiapparatus,lysosome,mitochondrion,nucleus,per-
oxisome,plasmamembrane,andvacuole.Fortheconstructionofthedataset,proteinsequences
werecollectedfromtheSWISS-PROTdatabase.IntheSWISS-PROTdatabase,wecheckedkeyword
informationaboutsubcellularlocationsintheCCfield,andalsocheckedtheOCfieldtoremove
prokaryoticproteins.Afterhomologycheck(80.0%),thetotalnumberofproteinsinthefinaldataset
was7589.
Fromtheproteinsequencedataset,asetofSupportVectorMachines(SVMs)wastrainedbased
onitsaminoacid,aminoacidpair,andfromonetothreegappedaminoacidpaircompositions.The
12SVMswerepreparedatfivedifferentcompositiondata.Thefeaturevectorhas20coordinatesfor
theaminoacidcompositionand400coordinatesforthefourkindsofaminoacidpaircompositions.
560Parketal.
Thepredictionmethodsbasedonthesefivedifferentcompositionswerethencombinedusingavoting
scheme.
Thepredictionperformancewasexaminedbythefive-foldcross-validationtest,inwhichthedata
setwasdividedintofivesubsetsofapproximatelyequalsize(Table1).Inordertoassesstheaccuracy
ofpredictionmethodsweusetwomeasures,thetotalaccuracy(TA)andthelocationaccuracy(LA)
definedby:

TA=k󰀁i=1Tik,
where:
Pi=
T
i

Accuracy12locations11locations10locations10locations
forplantcellsforfungalcellsforanimalcells

3Discussion
Resultsobtainedthroughfive-foldcrossvalidationtestsshowedanimprovementinpredictionaccuracy
overthealgorithmbasedontheaminoacidcompositionmainly[1].
Furtherpracticalpredictionmethodmaybeconstructedbyaddingnewsubcellularlocationsor
definingfinerclassifications,forexamplemitochondrialinner,outermembraneormatrixprotein
groups.Andsomeresearchersalsowantpredictionsystemforsomespecificlocationsonly.Wehave
toconsiderthesevariousneedsfromtheusers.Perhapsimprovementsofpredictionratecanbe
obtainedusingadditionalnewfeaturevectorsfortrainingofSVMs.

References
[1]Cai,Y.D.,Liu,X.J.,Xu,X.B.,andChou,K.C.,Supportvectormachinesforpredictionofprotein
subcellularlocationbyincorporatingquasi-sequence-ordereffect,J.Cell.Biochem.,84:343–348.
2002.
[2]Park,K.-J.andKanehisa,M.,Predictionofproteinsubcellularlocationsbysupportvector
machinesusingcompositionsofaminoacidsandaminoacidpairs,Bioinformatics,19(13):1656–
1663,2003.
[3]PLOC,http://www.genome.ad.jp/SIT/ploc.html