Biology:Competing endogenous RNA (ceRNA) databases and resources

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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]
.

References

  1. ↑ 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. PMID 21802130. 
  2. ↑ Tay, Y; Rinn, J; Pandolfi, PP (Jan 16, 2014). "The multilayered complexity of ceRNA crosstalk and competition.". Nature 505 (7483): 344–52. doi:10.1038/nature12986. PMID 24429633. 
  3. ↑ 3.0 3.1 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. PMID 24297251. 
  4. ↑ Sarver, AL; Subramanian, S (2012). "Competing endogenous RNA database.". Bioinformation 8 (15): 731–3. doi:10.6026/97320630008731. PMID 23055620. 
  5. ↑ 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. PMID 21037263. 
  6. ↑ Chiu, Hua-Sheng; Llobet-Navas, David; Yang, Xuerui; Chung, Wei-Jen; Ambesi-Impiombato, Alberto; Iyer, Archana; Kim, Hyunjae "Ryan"; Seviour, Elena G. et al. (February 2015). "Cupid: simultaneous reconstruction of microRNA-target and ceRNA networks". Genome Research 25 (2): 257–67. doi:10.1101/gr.178194.114. PMID 25378249. PMC 4315299. http://genome.cshlp.org/content/25/2/257. 
  7. ↑ Sumazin, P; Yang, X; Chiu, HS; Chung, WJ; Iyer, A; Llobet-Navas, D; Rajbhandari, P; Bansal, M et al. (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. PMID 22000015. 
  8. ↑ 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. 

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