Prediction of Body Fluids where Proteins are Secreted into Based on Protein Interaction Network 英文参考文献.docVIP

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Prediction of Body Fluids where Proteins are Secreted into Based on Protein Interaction Network 英文参考文献.doc

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Prediction of Body Fluids where Proteins are Secreted into Based on Protein Interaction Network 英文参考文献

PredictionofBodyFluidswhereProteinsareSecreted intoBasedonProteinInteractionNetwork Le-LeHu1,2,TaoHuang3,4,Yu-DongCai1,5,6*,Kuo-ChenChou6 1Institute of Systems Biology, Shanghai University, Shanghai, China, 2Department of Chemistry, College of Sciences, Shanghai University, Shanghai, China, 3Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China, 4Shanghai Center for Bioinformation Technology, Shanghai, China, 5Centre for Computational Systems Biology, Fudan University, Shanghai, China, 6Gordon Life Science Institute, San Diego, California, UnitedStatesofAmerica Abstract Determiningthebodyfluidswheresecretedproteinscanbesecretedintoisimportantforproteinfunctionannotationand disease biomarker discovery. In this study, we developed a network-based method to predict which kind of body fluids human proteins can be secreted into. For a newly constructed benchmark dataset that consists of 529 human-secreted proteins,thepredictionaccuracyforthemostpossiblebodyfluidlocationpredictedbyourmethodviathejackknifetest was79.02%,significantlyhigherthanthesuccessratebyarandomguess(29.36%).Thelikelihoodthatthepredictedbody fluidsofthefirstfourorderscontainallthetruebodyfluidswheretheproteinscanbesecretedintois62.94%.Ourmethod wasfurtherdemonstratedwithtwoindependentdatasets:onecontains57proteinsthatcanbesecretedintoblood;while the other contains 61 proteins that can be secreted into plasma/serum and were possible biomarkers associated with various cancers. For the 57 proteins in first dataset, 55 were correctly predicted as blood-secrete proteins. For the 61 proteinsintheseconddataset,58werepredictedtobemostpossibleinplasma/serum.Theseencouragingresultsindicate thatthenetwork-based predictionmethodisquitepromising.Itisanticipated thatthemethodwillbenefittherelevant areasforbothbasicresearchanddrugdevelopment. Citation: Hu L-L, Huang T, Cai Y-D, Chou K-C (2011) Prediction of Body Fluids where Proteins are Sec