CeRNA database
From Wikipedia, the free encyclopedia
Competing endogenous RNAs (ceRNAs, also refer as miRNA sponges) hypothesis: ceRNAs regulate other RNA transcripts (e.g., PTEN) by competing for shared microRNAs.[1] They are playing important roles in developmental, physiological and pathological processes, such as cancer. Multiple classes of ncRNAs (lncRNAs, circRNAs, pseudogenes) and protein-coding mRNAs function as key ceRNAs (sponges) and to regulate the expression of mRNAs in plants and mammalian cells.[2]
This competing endogenous RNA (ceRNA) databases and resources is a compilation of databases and web portals and servers used for ceRNA prediction and ceRNA networks.
| Name | Description | type | References |
|---|---|---|---|
| ceRNABase | ceRNABase is designed for decoding Pan-Cancer ceRNA networks involving lncRNAs and mRNAs by analyzing 5599 tumor and normal samples and 108 CLIP-Seq (HITS-CLIP, PAR-CLIP, iCLIP, CLASH) datasets. | database and server | [3] |
| cefinder | Competing endogenous RNA database: predicted ceRNA candidates from genome. | database | [4] |
| ceRNAFunction | ceRNAFunction is a web server to predict lncRNA and protein functions from pan-cancer ceRNA networks using 13 functional terms (including: GO, KEGG, BIOCARTA, etc.). | webserver | [3][5] |
| Cupid | Cupid is a method for simultaneous prediction of miRNA-target interactions and their mediated competing endogenous RNA (ceRNA) interactions. It is an integrative approach significantly improves on miRNA-target prediction accuracy as assessed by both mRNA and protein level measurements in breast cancer cell lines. Cupid is implemented in 3 steps: Step 1: re-evaluate candidate miRNA binding sites in 3' UTRs. Step2: interactions are predicted by integrating information about selected sites and the statistical dependency between the expression profiles of miRNA and putative targets. Step 3: Cupid assesses whether inferred targets compete for predicted miRNA regulators. | software (MATLAB) | [6] |
| Hermes | Hermes predicts ceRNA (competing endogenous RNA) interactions from expression profiles of candidate RNAs and their common miRNA regulators using conditional mutual information. | software (MATLAB) | [7] |
| Linc2GO | a human LincRNA function annotation resource based on ceRNA webserver. | database | [8] |
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