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Predicting the Functions of Long Noncoding RNAs Using RNA-Seq Based on Bayesian Network
Joint Authors
Li, Feng
Xiao, Yun
Lv, Yanling
Zhao, Hongying
Hu, Jing
Xu, Jinyuan
Bai, Jing
Yu, Fulong
Li, Xia
Gong, Yonghui
Source
Issue
Vol. 2015, Issue 2015 (31 Dec. 2015), pp.1-14, 14 p.
Publisher
Hindawi Publishing Corporation
Publication Date
2015-02-28
Country of Publication
Egypt
No. of Pages
14
Main Subjects
Abstract EN
Long noncoding RNAs (lncRNAs) have been shown to play key roles in various biological processes.
However, functions of most lncRNAs are poorly characterized.
Here, we represent a framework to predict functions of lncRNAs through construction of a regulatory network between lncRNAs and protein-coding genes.
Using RNA-seq data, the transcript profiles of lncRNAs and protein-coding genes are constructed.
Using the Bayesian network method, a regulatory network, which implies dependency relations between lncRNAs and protein-coding genes, was built.
In combining protein interaction network, highly connected coding genes linked by a given lncRNA were subsequently used to predict functions of the lncRNA through functional enrichment.
Application of our method to prostate RNA-seq data showed that 762 lncRNAs in the constructed regulatory network were assigned functions.
We found that lncRNAs are involved in diverse biological processes, such as tissue development or embryo development (e.g., nervous system development and mesoderm development).
By comparison with functions inferred using the neighboring gene-based method and functions determined using lncRNA knockdown experiments, our method can provide comparable predicted functions of lncRNAs.
Overall, our method can be applied to emerging RNA-seq data, which will help researchers identify complex relations between lncRNAs and coding genes and reveal important functions of lncRNAs.
American Psychological Association (APA)
Xiao, Yun& Lv, Yanling& Zhao, Hongying& Gong, Yonghui& Hu, Jing& Li, Feng…[et al.]. 2015. Predicting the Functions of Long Noncoding RNAs Using RNA-Seq Based on Bayesian Network. BioMed Research International،Vol. 2015, no. 2015, pp.1-14.
https://search.emarefa.net/detail/BIM-1056949
Modern Language Association (MLA)
Xiao, Yun…[et al.]. Predicting the Functions of Long Noncoding RNAs Using RNA-Seq Based on Bayesian Network. BioMed Research International No. 2015 (2015), pp.1-14.
https://search.emarefa.net/detail/BIM-1056949
American Medical Association (AMA)
Xiao, Yun& Lv, Yanling& Zhao, Hongying& Gong, Yonghui& Hu, Jing& Li, Feng…[et al.]. Predicting the Functions of Long Noncoding RNAs Using RNA-Seq Based on Bayesian Network. BioMed Research International. 2015. Vol. 2015, no. 2015, pp.1-14.
https://search.emarefa.net/detail/BIM-1056949
Data Type
Journal Articles
Language
English
Notes
Includes bibliographical references
Record ID
BIM-1056949