lnCeDB: database of human long noncoding RNA acting as competing endogenous RNA

PLoS One. 2014 Jun 13;9(6):e98965. doi: 10.1371/journal.pone.0098965. eCollection 2014.

Abstract

Long noncoding RNA (lncRNA) influences post-transcriptional regulation by interfering with the microRNA (miRNA) pathways, acting as competing endogenous RNA (ceRNA). These lncRNAs have miRNA responsive elements (MRE) in them, and control endogenous miRNAs available for binding with their target mRNAs, thus reducing the repression of these mRNAs. lnCeDB provides a database of human lncRNAs (from GENCODE 19 version) that can potentially act as ceRNAs. The putative mRNA targets of human miRNAs and the targets mapped to AGO clipped regions are collected from TargetScan and StarBase respectively. The lncRNA targets of human miRNAs (up to GENCODE 11) are downloaded from miRCode database. miRNA targets on the rest of the GENCODE 19 lncRNAs are predicted by our algorithm for finding seed-matched target sites. These putative miRNA-lncRNA interactions are mapped to the Ago interacting regions within lncRNAs. To find out the likelihood of an lncRNA-mRNA pair for actually being ceRNA we take recourse to two methods. First, a ceRNA score is calculated from the ratio of the number of shared MREs between the pair with the total number of MREs of the individual candidate gene. Second, the P-value for each ceRNA pair is determined by hypergeometric test using the number of shared miRNAs between the ceRNA pair against the number of miRNAs interacting with the individual RNAs. Typically, in a pair of RNAs being targeted by common miRNA(s), there should be a correlation of expression so that the increase in level of one ceRNA results in the increased level of the other ceRNA. Near-equimolar concentration of the competing RNAs is associated with more profound ceRNA effect. In lnCeDB one can not only browse for lncRNA-mRNA pairs having common targeting miRNAs, but also compare the expression of the pair in 22 human tissues to estimate the chances of the pair for actually being ceRNAs.

Availability: Downloadable freely from http://gyanxet-beta.com/lncedb/.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Computational Biology
  • Databases, Genetic*
  • Epistasis, Genetic
  • Gene Expression Regulation
  • Gene Regulatory Networks
  • Humans
  • MicroRNAs / genetics
  • RNA Interference*
  • RNA, Long Noncoding / physiology*
  • RNA, Messenger / genetics*
  • RNA, Messenger / metabolism

Substances

  • MicroRNAs
  • RNA, Long Noncoding
  • RNA, Messenger

Grants and funding

The authors received financial support from the intramural funds of their host institutes. SD, SG and JC received financial support from the Indian Association for the Cultivation of Science. RS was hosted by Gyanxet, an independent non-profit body. Funds for the website were contributed by Gyanxet. The fund giving organizations, namely, the Indian Association for the Cultivation of Science and Gyanxet, had no role in the design, data collection and analysis, the decision to publish, or in the preparation of the manuscript.