Competing endogenous RNAs (ceRNAs, also refer as miRNA sponges) hypothesis: ceRNAs regulate other RNA transcripts (e.g., PTEN) by competing for shared microRNAs. 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.
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 | |
| cefinder | Competing endogenous RNA database: predicted ceRNA candidates from genome. | database | |
| 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 | |
| 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) | |
| 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) | |
| Linc2GO | a human LincRNA function annotation resource based on ceRNA webserver. | database | |
| . | |||
References
- Salmena, L; Poliseno, L; Tay, Y; Kats, L; Pandolfi, PP (Aug 5, 2011). "A ceRNA hypothesis: the Rosetta Stone of a hidden RNA language?". Cell. 146 (3): 353–8. doi:10.1016/j.cell.2011.07.014. PMC 3235919. PMID 21802130.
- Tay, Y; Rinn, J; Pandolfi, PP (Jan 16, 2014). "The multilayered complexity of ceRNA crosstalk and competition". Nature. 505 (7483): 344–52. Bibcode:2014Natur.505..344T. doi:10.1038/nature12986. PMC 4113481. PMID 24429633.
- ^ Li, JH; Liu, S; Zhou, H; Qu, LH; Yang, JH (Jan 1, 2014). "starBase v2.0: decoding miRNA-ceRNA, miRNA-ncRNA and protein-RNA interaction networks from large-scale CLIP-Seq data". Nucleic Acids Research. 42 (1): D92–7. doi:10.1093/nar/gkt1248. PMC 3964941. PMID 24297251.
- Sarver, AL; Subramanian, S (2012). "Competing endogenous RNA database". Bioinformation. 8 (15): 731–3. doi:10.6026/97320630008731. PMC 3449376. PMID 23055620.
- Yang, J. -H.; Li, J. -H.; Shao, P.; Zhou, H.; Chen, Y. -Q.; Qu, L. -H. (2010). "StarBase: A database for exploring microRNA-mRNA interaction maps from Argonaute CLIP-Seq and Degradome-Seq data". Nucleic Acids Research. 39 (Database issue): D202 – D209. doi:10.1093/nar/gkq1056. PMC 3013664. PMID 21037263.
- Chiu, Hua-Sheng; Llobet-Navas, David; Yang, Xuerui; Chung, Wei-Jen; Ambesi-Impiombato, Alberto; Iyer, Archana; Kim, Hyunjae "Ryan"; Seviour, Elena G.; Luo, Zijun; Sehgal, Vasudha; Moss, Tyler; Lu, Yiling; Ram, Prahlad; Silva, José; Mills, Gordon B.; Califano, Andrea; Sumazin, Pavel (February 2015). "Cupid: simultaneous reconstruction of microRNA-target and ceRNA networks". Genome Research. 25 (2): 257–67. doi:10.1101/gr.178194.114. PMC 4315299. PMID 25378249.
- Sumazin, P; Yang, X; Chiu, HS; Chung, WJ; Iyer, A; Llobet-Navas, D; Rajbhandari, P; Bansal, M; Guarnieri, P; Silva, J; Califano, A (Oct 14, 2011). "An extensive microRNA-mediated network of RNA-RNA interactions regulates established oncogenic pathways in glioblastoma". Cell. 147 (2): 370–81. doi:10.1016/j.cell.2011.09.041. PMC 3214599. PMID 22000015.
- Liu, K; Yan, Z; Li, Y; Sun, Z (Sep 1, 2013). "Linc2GO: a human LincRNA function annotation resource based on ceRNA hypothesis". Bioinformatics. 29 (17): 2221–2. doi:10.1093/bioinformatics/btt361. PMID 23793747.