LncRRIsearch: A Web Server for lncRNA-RNA Interaction Prediction Integrated With Tissue-Specific Expression and Subcellular Localization Data

Tsukasa Fukunaga; Junichi Iwakiri; Yukiteru Ono; Michiaki Hamada

doi:10.3389/fgene.2019.00462

LncRRIsearch: A Web Server for lncRNA-RNA Interaction Prediction Integrated With Tissue-Specific Expression and Subcellular Localization Data

Front Genet. 2019 May 28:10:462. doi: 10.3389/fgene.2019.00462. eCollection 2019.

Authors

Tsukasa Fukunaga^{1

2}, Junichi Iwakiri^{3

4}, Yukiteru Ono⁵, Michiaki Hamada^{1

4

6

7

8

9}

Affiliations

¹ Department of Electrical Engineering and Bioscience, Faculty of Science and Engineering, Waseda University, Tokyo, Japan.
² Department of Computer Science, Graduate School of Information Science and Technology, The University of Tokyo, Tokyo, Japan.
³ Graduate School of Frontier Sciences, University of Tokyo, Chiba, Japan.
⁴ Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan.
⁵ IMSBIO Co., Ltd., Tokyo, Japan.
⁶ Computational Bio Big-Data Open Innovation Laboratory, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan.
⁷ Institute for Medical-oriented Structural Biology, Waseda University, Tokyo, Japan.
⁸ Graduate School of Medicine, Nippon Medical School, Tokyo, Japan.
⁹ Center for Data Science, Waseda University, Tokyo, Japan.

Abstract

Long non-coding RNAs (lncRNAs) play critical roles in various biological processes, but the function of the majority of lncRNAs is still unclear. One approach for estimating a function of a lncRNA is the identification of its interaction target because functions of lncRNAs are expressed through interaction with other biomolecules in quite a few cases. In this paper, we developed "LncRRIsearch," which is a web server for comprehensive prediction of human and mouse lncRNA-lncRNA and lncRNA-mRNA interaction. The prediction was conducted using RIblast, which is a fast and accurate RNA-RNA interaction prediction tool. Users can investigate interaction target RNAs of a particular lncRNA through a web interface. In addition, we integrated tissue-specific expression and subcellular localization data for the lncRNAs with the web server. These data enable users to examine tissue-specific or subcellular localized lncRNA interactions. LncRRIsearch is publicly accessible at http://rtools.cbrc.jp/LncRRIsearch/.

Keywords: RNA-RNA interaction; lncRNA; subcellular localization; tissue-specific expression; web server.