MiRSponge: a manually curated database for experimentally supported miRNA sponges and ceRNAs.

Peng Wang,Yunpeng Zhang,Maoni Guo,Shangwei Ning,Jizhou Zhang,Yue Gao,Hui Zhi,Xia Li,Yue Liu

doi:10.1093/database/bav098

Peng Wang, Yunpeng Zhang + Show 7 more

Open Access

https://doi.org/10.1093/database/bav098

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Abstract

In this study, we describe miRSponge, a manually curated database, which aims at providing an experimentally supported resource for microRNA (miRNA) sponges. Recent evidence suggests that miRNAs are themselves regulated by competing endogenous RNAs (ceRNAs) or ‘miRNA sponges’ that contain miRNA binding sites. These competitive molecules can sequester miRNAs to prevent them interacting with their natural targets to play critical roles in various biological and pathological processes. It has become increasingly important to develop a high quality database to record and store ceRNA data to support future studies. To this end, we have established the experimentally supported miRSponge database that contains data on 599 miRNA-sponge interactions and 463 ceRNA relationships from 11 species following manual curating from nearly 1200 published articles. Database classes include endogenously generated molecules including coding genes, pseudogenes, long non-coding RNAs and circular RNAs, along with exogenously introduced molecules including viral RNAs and artificial engineered sponges. Approximately 70% of the interactions were identified experimentally in disease states. miRSponge provides a user-friendly interface for convenient browsing, retrieval and downloading of dataset. A submission page is also included to allow researchers to submit newly validated miRNA sponge data.Database URL: http://www.bio-bigdata.net/miRSponge.

Highlights

MicroRNAs are a class of small (19–25 nt) noncoding RNAs that regulate their target genes by binding to and targeting mRNAs for degradation or by inhibiting protein translation at the post-transcriptional level [1]. miRNAs are involved in many biological processes [2,3,4], and aberrant expression of miRNAs has been implicated in numerous diseases including cancers [2]
Emerging evidence suggests that miRNAs are themselves regulated by other RNA molecules that contain complementary miRNA binding sites, such as mRNAs, pseudogenes, long noncoding RNAs and circular RNAs [5,6,7]
These miRNA-binding RNAs or ‘miRNA sponges’ are competitive regulators that sequester miRNAs which prevents them interacting with their intended targets [8,9,10]. miRNA sponges are known as competing endogenous RNAs, and they act dynamically to regulate the expression of each other via competing mechanisms that are important for various physiological and pathological processes

Summary

Introduction

MicroRNAs (miRNAs) are a class of small (19–25 nt) noncoding RNAs that regulate their target genes by binding to and targeting mRNAs for degradation or by inhibiting protein translation at the post-transcriptional level [1]. miRNAs are involved in many biological processes [2,3,4], and aberrant expression of miRNAs has been implicated in numerous diseases including cancers [2]. All associated data sources, including sequence information, experimental validated datasets, functional annotation data, scores and thermodynamic free energy of predicted miRNA targets, can be freely downloaded from the miRSponge ‘Download’ page. A literature search of the LncRNADisease database [37] found that most of these pathways were previously associated with H19 (Figure 3C), confirming that H19 is an important regulator in many types of cancers and can be used as a potential tumor marker for initial diagnosis and monitoring of therapies. This further confirmed the usefulness of the miRSponge database. These tools will identify miRNA-sponge/ceRNA interactions via a bioinformatics pipeline that integrates several in silico target predictions, Ago-CLIP experimental data, and expression profiling from transcriptome sequencing experiments

Methodology

Findings

Discussion and Conclusions