CeRNA database explained

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	^[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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Notes and References

1. Salmena. L. Poliseno, L . Tay, Y . Kats, L . Pandolfi, PP . A ceRNA hypothesis: the Rosetta Stone of a hidden RNA language?. Cell. Aug 5, 2011. 146. 3. 353–8. 21802130 . 10.1016/j.cell.2011.07.014 . 3235919.
2. Tay. Y. Rinn, J . Pandolfi, PP . The multilayered complexity of ceRNA crosstalk and competition.. Nature. Jan 16, 2014. 505. 7483. 344–52. 24429633. 10.1038/nature12986. 4113481. 2014Natur.505..344T.
3. Li. JH. Liu, S . Zhou, H . Qu, LH . Yang, JH . starBase v2.0: decoding miRNA-ceRNA, miRNA-ncRNA and protein-RNA interaction networks from large-scale CLIP-Seq data.. Nucleic Acids Research. Jan 1, 2014. 42. 1. D92–7. 24297251. 10.1093/nar/gkt1248 . 3964941.
4. Sarver. AL. Subramanian, S. Competing endogenous RNA database.. Bioinformation. 2012. 8. 15. 731–3. 23055620. 10.6026/97320630008731. 3449376.
5. Yang . J. -H. . Li . J. -H. . Shao . P. . Zhou . H. . Chen . Y. -Q. . Qu . L. -H. . 10.1093/nar/gkq1056 . 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 . 2010 . 21037263. 3013664 .
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. Cupid: simultaneous reconstruction of microRNA-target and ceRNA networks. Genome Research. February 2015. 25. 2. 257–67. 10.1101/gr.178194.114. 25378249. 4315299.
7. Sumazin. P . Yang, X . Chiu, HS . Chung, WJ . Iyer, A . Llobet-Navas, D . Rajbhandari, P . Bansal, M . Guarnieri, P . Silva, J . Califano, A. An extensive microRNA-mediated network of RNA-RNA interactions regulates established oncogenic pathways in glioblastoma.. Cell. Oct 14, 2011. 147. 2. 370–81. 22000015. 10.1016/j.cell.2011.09.041. 3214599.
8. Liu. K. Yan, Z . Li, Y . Sun, Z . Linc2GO: a human LincRNA function annotation resource based on ceRNA hypothesis.. Bioinformatics. Sep 1, 2013. 29. 17. 2221–2. 23793747 . 10.1093/bioinformatics/btt361. free.