Welcome to the lnCeDB
Long noncoding RNA (lncRNA) can influence post-transcriptional regulation by interfering with the miRNA pathways, i.e. acting as competing endogenous RNA (ceRNA). These lncRNAs have miRNA binding sites in them and control endogenous miRNAs available for binding their target mRNAs, thus reducing the repression of these mRNAs.
lnCeDB provides for the first time, a database of human lncRNAs (from the latest GENCODE 19 version) that can potentially act as ceRNAs. The mRNA targets of human miRNAs are predicted by Targetscan and mapped to par-clip data (downloaded from StarBase). The lncRNA targets of human miRNAs (upto GENCODE 11 lncRNAs) 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. Typically, in a pair of RNAs being targeted by common miRNA(s), there should be a correlation of expression. The expression of the ceRNA in the respective tissue should be high enough to affect the cellular level of the available targeting miRNA, so that the repression level of its competing ceRNA can be reduced. 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 (from RNA-Seq expression data from Cabili et al) to estimate the chances of the pair for actually being ceRNAs.