LIVE: a manually curated encyclopedia of experimentally validated interactions of lncRNAs.

Gaole An,Xiaochen Bo,Zhangyi Ouyang,Chao Ren,Wenjie Shu,Jiaqi Sun,Shaoliang Peng,Lingyun Zhu

doi:10.1093/database/baz011

Abstract

Advances in studies of long noncoding RNAs (lncRNAs) have provided data regarding the regulatory roles of lncRNAs, which perform functional roles through interactions with other functional elements. To track the underlying relationships among lncRNAs, various databases have been developed as repositories for lncRNA data. However, the ability to comprehensively explore the diverse interactions between lncRNAs and other functional elements is limited. To this end, we developed LIVE (LncRNA Interaction Validated Encyclopaedia), an interactive resource to integrate the diverse interactions of functional elements with lncRNAs. LIVE is a manually curated database of experimentally validated interactions of lncRNAs with genes, proteins and other various functional elements. By mining publications, we constructed LIVE with the following three interaction networks: a binding interaction network, a regulation network and a disease network; then, we combined them to form a comprehensive lncRNA interaction network. The current release of LIVE contains the validated interactions of 572 lncRNAs in humans and mice with 103 proteins, 209 genes, 56 transcription factors and 194 diseases. LIVE provides an interactive interface with charts and figures to aid users in searching and browsing interactions with lncRNAs. LIVE will greatly facilitate further investigation into the regulatory roles of lncRNAs and is freely available.

Highlights

LncRNAs play important functional roles in regulating biological and cellular processes, including proliferation, differentiation and development, through interacting with various genes, proteins and functional elements [1, 2]
Unlike the early databases developed to deposit candidate long noncoding RNAs (lncRNAs) from both experimental validation and computational prediction studies, recent databases have focused on the specific functional roles of lncRNAs
By mining and manually curating publications to extract experimentally validated interactions, we generated LIVE, which presents the comprehensive interactions of lncRNAs with genes, proteins, ncRNAs, transcription factors and diseases in humans and mice

Summary

Introduction

LncRNAs play important functional roles in regulating biological and cellular processes, including proliferation, differentiation and development, through interacting with various genes, proteins and functional elements [1, 2]. LncReg collects the validated regulatory relationships of lncRNAs [4]. Lnc2Meth was developed to store relationships between human lncRNAs and DNA methylation [5]. LncChrom includes validated lncRNAchromatin interactions [6]. These databases face accuracy problems due to the high false positive rate of data from computational predictions and high-throughput experiments. There is still an urgent demand for an experimentally validated lncRNA database that has been manually curated. EVlncRNAs manually curated publications to include experimentally validated lncRNA interactions [7], but the potential interaction networks beneath publications are not fully revealed

Methods

Results

Conclusion