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

doi:10.3389/fgene.2018.00096

	FSPP: A Tool for Genome-Wide Prediction of smORF-Encoded Peptides and Their Functions
	Li, Hui 1,2; Xiao, Li 1; Zhang, Lili 2,3; Wu, Jiarui 4; Wei, Bin 1; Sun, Ninghui 5; Zhao, Yi 1
	2018-04-05
发表期刊	FRONTIERS IN GENETICS
ISSN	1664-8021
卷号	9 页码:8
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.
关键词	smORF SEP Ribo-seq MS function
DOI	10.3389/fgene.2018.00096
收录类别	SCI
语种	英语
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
WOS类目	Genetics & Heredity
WOS记录号	WOS:000429261800001
出版者	FRONTIERS MEDIA SA
引用统计	被引频次：46[WOS] [WOS记录] [WOS相关记录]
文献类型	期刊论文
条目标识符	http://119.78.100.204/handle/2XEOYT63/5931
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 Comp Technol, Adv Comp Res Ctr, Key Lab Intelligent Informat Proc, Beijing, Peoples R China 2.Univ Chinese Acad Sci, Sch Comp & Control Engn, Beijing, Peoples R China 3.Chinese Acad Sci, Inst Biophys, CAS Key Lab RNA Biol, Beijing, Peoples R China 4.Beijing Univ Chinese Med, Sch Chinese Mat Med, Dept Clin Pharmacol Tradit Chinese Med, Beijing, Peoples R China 5.Chinese Acad Sci, Inst Comp Technol, State Key Lab Comp Architecture, 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.