Gene Ontology(GO)has been widely used to annotate functions of genes and gene prod-ucts.Here,we proposed a new method,TripletGO,to deduce GO terms of protein-coding and non-coding genes,through the integration of four complementary pipelines built on transcript expression profile,genetic sequence alignment,protein sequence alignment,and naive probability.TripletGO was tested on a large set of 5754 genes from 8 species(human,mouse,Arabidopsis,rat,fly,budding yeast,fission yeast,and nematoda)and 2433 proteins with available expression data from the third Critical Assessment of Protein Function Annotation challenge(CAFA3).Experimental results show that TripletGO achieves function annotation accuracy significantly beyond the current state-of-the-art approaches.Detailed analyses show that the major advantage of TripletGO lies in the coupling of a new triplet network-based profiling method with the feature space mapping technique,which can accurately recognize function patterns from transcript expression profiles.Meanwhile,the combination of multiple complementary models,especially those from transcript expression and protein-level alignments,improves the coverage and accuracy of the final GO anno-tation results.The standalone package and an online server of TripletGO are freely available at .

Yi-Heng Zhu;Chengxin Zhang;Yan Liu;Gilbert S.Omenn;Peter L.Freddolino;Dong-Jun Yu;Yang Zhang

School of Computer Science and Engineering,Nanjing University of Science and Technology,Nanjing 210094,China;Department of Computational Medicine and Bioinformatics,University of Michigan,Ann Arbor,MI 48109,USA;Departments of Internal Medicine and Human Genetics,and School of Public Health,University of Michigan,Ann Arbor,MI 48109,USA;Department of Biological Chemistry,University of Michigan,Ann Arbor,MI 48109,USA

基因组蛋白质组与生物信息学报（英文版）

[1]Yi-Heng Zhu;Chengxin Zhang;Yan Liu;Gilbert S.Omenn;Peter L.Freddolino;Dong-Jun Yu;Yang Zhang-.TripletGO:Integrating Transcript Expression Profiles with Protein Homology Inferences for Gene Function Prediction)[J].基因组蛋白质组与生物信息学报（英文版）,2022(05):1013-1027

TripletGO,Inferences,annotate,nematoda,CAFA3,anno

Integrating,Transcript,Expression,Profiles,Protein,Homology,Gene,Function,Prediction,Ontology,has,been,widely,used,functions,genes,prod,ucts,Here,we,proposed,new,method,deduce,terms,coding,through,integration,four,complementary,pipelines,built,transcript,expression,genetic,sequence,naive,probability,was,tested,large,set,from,species,human,mouse,Arabidopsis,fly,budding,yeast,fission,proteins,available,data,third,Critical,Assessment,Annotation,challenge,Experimental,results,show,that,achieves,annotation,accuracy,significantly,beyond,current,state,art,approaches,Detailed,analyses,major,advantage,lies,coupling,triplet,network,profiling,feature,space,mapping,technique,which,accurately,recognize,patterns,profiles,Meanwhile,combination,multiple,models,especially,those,level,alignments,improves,coverage,final,standalone,package,online,server,are,freely

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