Computational prediction of associations between long non-coding RNAs and proteins.
BACKGROUND
Though most of the transcripts are long non-coding RNAs (lncRNAs), little is known about their functions. lncRNAs usually function through interactions with proteins, which implies the importance of identifying the binding proteins of lncRNAs in understanding the molecular mechanisms underlying the functions of lncRNAs. Only a few approaches are available for predicting interactions between lncRNAs and proteins. In this study, we introduce a new method lncPro.


RESULTS
By encoding RNA and protein sequences into numeric vectors, we used matrix multiplication to score each RNA-protein pair. This score can be used to measure the interactions between an RNA-protein pair. This method effectively discriminates interacting and non-interacting RNA-protein pairs and predicts RNA-protein interactions within a given complex. Applying this method on all human proteins, we found that the long non-coding RNAs we collected tend to interact with nuclear proteins and RNA-binding proteins.


CONCLUSIONS
Compared with the existing approaches, our method shortens the time for training matrix and obtains optimal results based on the model being used. The ability of predicting the associations between lncRNAs and proteins has also been enhanced. Our method provides an idea on how to integrate different information into the prediction process.
Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China. litt@hsc.pku.edu.cn.
Qiongshi
Q
Lu
Sijin
S
Ren
Ming
M
Lu
Yong
Y
Zhang
Dahai
D
Zhu
Xuegong
X
Zhang
Tingting
T
Li
D000595:Amino Acid Sequence; D001483:Base Sequence; D019295:Computational Biology / Q000379:methods*; D030561:Databases, Nucleic Acid; D005822:Genetic Vectors / Q000235:genetics; D006801:Humans; D009687:Nuclear Proteins / Q000235:genetics / Q000378:metabolism*; D011485:Protein Binding; D062085:RNA, Long Noncoding / Q000378:metabolism*; D016601:RNA-Binding Proteins / Q000378:metabolism*; D015203:Reproducibility of Results
D009687:Nuclear Proteins; D062085:RNA, Long Noncoding; D016601:RNA-Binding Proteins