Frequently Asked Questions

What is ceRNA?

In recent years it has been discovered that endogenous RNAs (mRNAs, pseudogenes or long noncoding RNAs) can compete with each other for a limited pool of cellular microRNAs (miRNAs) and thus affect the competing RNA’s level. This class of RNAs competing for common miRNA(s) are called competing endogenous RNA or ceRNA.

Usage of lnCeDB

Are there evidences of lncRNAs working as ceRNAs?

There are examples of lncRNAs that acts as ceRNAs to fine tune the expression of their competing mRNAs. For example lncRNA HULC is identified to modulate its self regulation in hepatocellular carcinoma by a ceRNA function and lincRNA-MD1 works as miRNA sponge to block miR-133 from binding to transcription factors involved in myogenic differentiation.

How reliable is the ceRNAs predicted in lnCeDB?

We have used mRNA-miRNA interactions from StarBase that stores miRNA targets predicted from CLIP-Seq data (Yang et al, 2011) and included the miRNA-lncRNA interactions predicted from PAR-CLIP data (Jalali et al, 2013). This limits the target search within regions of AGO interaction, thus significantly reducing false-positive target detection. ceRNAs specifically corresponding to PAR-CLIP supported miRNA target interactions are browsable in lnCeDB. Moreover, the chances of an lncRNA-mRNA pair for actually being ceRNA depends not only on the fact that they are targeted by common miRNA(s), but also on the number of distinct miRNAs targeting both transcripts and the concentration of the competing RNAs (Ala et al, 2013). In lnCeDB users can browse for lncRNA-mRNA pairs targeted by common miRNAs and compare the expression of the pair in 22 human tissues to estimate the chances of the pair for actually being ceRNAs.

A statistics of the data available in lnCeDB