Competing endogenous RNAs (ceRNAs, also refer as miRNA sponges) hypothesis: ceRNAs regulate other RNA transcripts (e.g., PTEN) by competing for shared microRNAs.[{{cite journal|last=Salmena|first=L|author2=Poliseno, L |author3=Tay, Y |author4=Kats, L |author5= Pandolfi, PP |title=A ceRNA hypothesis: the Rosetta Stone of a hidden RNA language?|journal=Cell|date=Aug 5, 2011|volume=146|issue=3|pages=353–8|pmid=21802130 |doi=10.1016/j.cell.2011.07.014 |pmc=3235919}}] 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.[{{cite journal|last=Tay|first=Y|author2=Rinn, J |author3=Pandolfi, PP |title=The multilayered complexity of ceRNA crosstalk and competition.|journal=Nature|date=Jan 16, 2014|volume=505|issue=7483|pages=344–52|pmid=24429633|doi=10.1038/nature12986|pmc=4113481|bibcode=2014Natur.505..344T}}]
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.
| class="wikitable"
! 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 | [{{cite journal|last=Li|first=JH|author2=Liu, S |author3=Zhou, H |author4=Qu, LH |author5= Yang, JH |title=starBase v2.0: decoding miRNA-ceRNA, miRNA-ncRNA and protein-RNA interaction networks from large-scale CLIP-Seq data.|journal=Nucleic Acids Research|date=Jan 1, 2014|volume=42|issue=1|pages=D92–7|pmid=24297251|doi=10.1093/nar/gkt1248 |pmc=3964941}}] |
| cefinder
|Competing endogenous RNA database: predicted ceRNA candidates from genome. | database | [{{cite journal|last=Sarver|first=AL|author2=Subramanian, S|title=Competing endogenous RNA database.|journal=Bioinformation|year=2012|volume=8|issue=15|pages=731–3|pmid=23055620|doi=10.6026/97320630008731|pmc=3449376}}] |
| 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 | [{{Cite journal | last1 = Yang | first1 = J. -H. | last2 = Li | first2 = J. -H. | last3 = Shao | first3 = P. | last4 = Zhou | first4 = H. | last5 = Chen | first5 = Y. -Q. | last6 = Qu | first6 = L. -H. | doi = 10.1093/nar/gkq1056 | title = StarBase: A database for exploring microRNA-mRNA interaction maps from Argonaute CLIP-Seq and Degradome-Seq data | journal = Nucleic Acids Research | volume = 39 | issue = Database issue | pages = D202–D209 | year = 2010 | pmid = 21037263| pmc =3013664 }}] |
| 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) | [{{cite journal|last1=Chiu|first1=Hua-Sheng|last2=Llobet-Navas|first2=David|last3=Yang|first3=Xuerui|last4=Chung|first4=Wei-Jen|last5=Ambesi-Impiombato|first5=Alberto|last6=Iyer|first6=Archana|last7=Kim|first7=Hyunjae "Ryan"|last8=Seviour|first8=Elena G.|last9=Luo|first9=Zijun|last10=Sehgal|first10=Vasudha|last11=Moss|first11=Tyler|last12=Lu|first12=Yiling|last13=Ram|first13=Prahlad|last14=Silva|first14=José|last15=Mills|first15=Gordon B.|last16=Califano|first16=Andrea|last17=Sumazin|first17=Pavel|title=Cupid: simultaneous reconstruction of microRNA-target and ceRNA networks|journal=Genome Research|date=February 2015|volume=25|issue=2|pages=257–67|doi=10.1101/gr.178194.114|pmid=25378249|url=http://genome.cshlp.org/content/25/2/257|pmc=4315299}}] |
| 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) | [{{cite journal|last=Sumazin|first=P |author2=Yang, X |author3=Chiu, HS |author4=Chung, WJ |author5=Iyer, A |author6=Llobet-Navas, D |author7=Rajbhandari, P |author8=Bansal, M |author9=Guarnieri, P |author10=Silva, J |author11=Califano, A|title=An extensive microRNA-mediated network of RNA-RNA interactions regulates established oncogenic pathways in glioblastoma.|journal=Cell|date=Oct 14, 2011|volume=147|issue=2|pages=370–81|pmid=22000015|doi=10.1016/j.cell.2011.09.041|pmc=3214599}}] |
| Linc2GO
|a human LincRNA function annotation resource based on ceRNA webserver. | database | [{{cite journal|last=Liu|first=K|author2=Yan, Z |author3=Li, Y |author4= Sun, Z |title=Linc2GO: a human LincRNA function annotation resource based on ceRNA hypothesis.|journal=Bioinformatics|date=Sep 1, 2013|volume=29|issue=17|pages=2221–2|pmid=23793747 |doi=10.1093/bioinformatics/btt361|doi-access=free}}] |
| colspan="4" | . |