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FSPP: A Tool for Genome-Wide Prediction of smORF-Encoded Peptides and Their Functions

文献类型：期刊论文

作者Li, Hui3,4; Xiao, Li3; Zhang, Lili1,4; Wu, Jiarui5; Wei, Bin3; Sun, Ninghui2; Zhao, Yi3
刊名FRONTIERS IN GENETICS
出版日期2018-04-05
卷号9页码:8
关键词smORF SEP Ribo-seq MS function
ISSN号1664-8021
DOI10.3389/fgene.2018.00096
英文摘要smORFs are small open reading frames of less than 100 codons. Recent low throughput experiments showed a lot of smORF-encoded peptides (SEPs) played crucial rule in processes such as regulation of transcription or translation, transportation through membranes and the antimicrobial activity. In order to gather more functional SEPs, it is necessary to have access to genome-wide prediction tools to give profound directions for low throughput experiments. In this study, we put forward a functional smORF-encoded peptides predictor (FSPP) which tended to predict authentic SEPs and their functions in a high throughput method. FSPP used the overlap of detected SEPs from Ribo-seq and mass spectrometry as target objects. With the expression data on transcription and translation levels, FSPP built two co-expression networks. Combing co-location relations, FSPP constructed a compound network and then annotated SEPs with functions of adjacent nodes. Tested on 38 sequenced samples of 5 human cell lines, FSPP successfully predicted 856 out of 960 annotated proteins. Interestingly, FSPP also highlighted 568 functional SEPs from these samples. After comparison, the roles predicted by FSPP were consistent with known functions. These results suggest that FSPP is a reliable tool for the identification of functional small peptides. FSPP source code can be acquired at https://www.bioinfo.org/FSPP.
资助项目National Natural Science Foundation of China[91740113] ; National Natural Science Foundation of China[31701149] ; National Natural Science Foundation of China[31401119] ; National Natural Science Foundation of China[31371320] ; National Natural Science Foundation of China[61472397] ; National Natural Science Foundation of China[31501066] ; CAS Pioneer Hundred Talents Program[2017-074]
WOS研究方向Genetics & Heredity
语种英语
WOS记录号WOS:000429261800001
出版者FRONTIERS MEDIA SA
源URL[http://119.78.100.204/handle/2XEOYT63/5930]  
专题中国科学院计算技术研究所期刊论文_英文
通讯作者Sun, Ninghui; Zhao, Yi
作者单位1.Chinese Acad Sci, Inst Biophys, CAS Key Lab RNA Biol, Beijing, Peoples R China
2.Chinese Acad Sci, Inst Comp Technol, State Key Lab Comp Architecture, Beijing, Peoples R China
3.Chinese Acad Sci, Inst Comp Technol, Adv Comp Res Ctr, Key Lab Intelligent Informat Proc, Beijing, Peoples R China
4.Univ Chinese Acad Sci, Sch Comp & Control Engn, Beijing, Peoples R China
5.Beijing Univ Chinese Med, Sch Chinese Mat Med, Dept Clin Pharmacol Tradit Chinese Med, Beijing, Peoples R China
推荐引用方式
GB/T 7714		 Li, Hui,Xiao, Li,Zhang, Lili,et al. FSPP: A Tool for Genome-Wide Prediction of smORF-Encoded Peptides and Their Functions[J]. FRONTIERS IN GENETICS,2018,9:8.
APA Li, Hui.,Xiao, Li.,Zhang, Lili.,Wu, Jiarui.,Wei, Bin.,...&Zhao, Yi.(2018).FSPP: A Tool for Genome-Wide Prediction of smORF-Encoded Peptides and Their Functions.FRONTIERS IN GENETICS,9,8.
MLA Li, Hui,et al."FSPP: A Tool for Genome-Wide Prediction of smORF-Encoded Peptides and Their Functions".FRONTIERS IN GENETICS 9(2018):8.

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来源：计算技术研究所

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