Competing endogenous RNA databases | Non-coding transcript data analysis
Competition for microRNA (miRNA) binding between RNA molecules has emerged as a novel mechanism for the regulation of eukaryotic gene expression. Competing endogenous RNA (ceRNA) can act as decoys for miRNA binding, thereby forming a ceRNA network by regulating the abundance of other RNA transcripts which share the same or similar microRNA response elements.
Lists potential miRNA response elements (MRE) containing genes that can act in a sponge like fashion (absorbing and releasing miRNA based on the level of the transcript) for a given mRNA based on a set of scoring and ranking criteria. ceRDB, for each mRNA, defines an interaction score by adding up the total number of miRNA binding sites that overlap with the miRNA for a given mRNA. This interaction score is used to sort the results and the top 50 predicted potential ceRNAs are returned. This process is carried out on the fly using PHP interactions with the mySQL database.
Provides resources to decode Pan-Cancer and Interaction Networks of lncRNAs, miRNAs, competing endogenous RNAs(ceRNAs), RNA-binding proteins (RBPs) and mRNAs from large-scale CLIP-Seq data and tumor samples. starBase deciphers Protein-RNA and miRNA-target interactions, such as protein-lncRNA, protein-sncRNA, protein-mRNA, protein-pseudogene, miRNA-lncRNA, miRNA-mRNA, miRNA-circRNA, miRNA-pseudogene, miRNA-sncRNA interactions and ceRNA networks from 108 CLIP-Seq datasets.
Provides a database of human lncRNAs (from GENCODE 19 version) that can potentially act as ceRNAs. 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.
Contains potential competing endogenous RNA (ceRNA) target-target, and ceRNA target-mimic pairs from 26 plant species. PceRBase also stores predicted pairing structure between miRNAs and their target mRNA transcripts, expression levels of ceRNA pairs and associated gene annotation (GO). A web interface provides convenient browsing and searching for specific genes of interest. Tools are available for the visualization and enrichment analysis of genes in the ceRNA networks. Moreover, users can use PceRBase to predict novel competing mimic-target and target–target interactions from their own data.