CeRNA database

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

^ 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.
^ ^a ^b 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.

[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. PMC 3235919. 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. Bibcode:2014Natur.505..344T. doi:10.1038/nature12986. PMC 4113481. PMID 24429633.

[Li_D92-7-3] 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.

[4] Sarver, AL; Subramanian, S (2012). "Competing endogenous RNA database". Bioinformation. 8 (15): 731–3. doi:10.6026/97320630008731. PMC 3449376. PMID 23055620.

[pmid21037263-5] 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. PMC 3013664. PMID 21037263.

[Chiu_et._al,_Genome_Res_2015-6] 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.

[7] 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.

[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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