CeRNA database
Competing endogenous RNAs (ceRNAs) 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. (Salmena et al. 2011 Cell). 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.
competing endogenous RNA (ceRNA) databases and resources
| Name | Description | type | Link | 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 | website | [1][2] |
| [cefinder] | Competing endogenous RNA database: predicted ceRNA candidates from genome. | database | website | [3] |
| [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 | webserver | [1][4] |
| [Linc2GO] | a human LincRNA function annotation resource based on ceRNA webserver. | database | website | [5] |
| [HERMES] | Hermes predicts ceRNA (competing endogenous RNA) interactions from expression profiles of candidate RNAs and their common miRNA regulators using conditional mutual information. | softwares | website | [6] |
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- ^ a b Attention: This template ({{cite doi}}) is deprecated. To cite the publication identified by doi:10.1093/nar/gkq1056, please use {{cite journal}} (if it was published in a bona fide academic journal, otherwise {{cite report}} with
|doi=10.1093/nar/gkq1056instead. - ^ Li, JH (2014 Jan 1). "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.
{{cite journal}}: Check date values in:|date=(help); Unknown parameter|coauthors=ignored (|author=suggested) (help) - ^ Sarver, AL (2012). "Competing endogenous RNA database". Bioinformation. 8 (15): 731–3. PMID 23055620.
{{cite journal}}: Unknown parameter|coauthors=ignored (|author=suggested) (help) - ^ Li, JH (2014 Jan 1). "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.
{{cite journal}}: Check date values in:|date=(help); Unknown parameter|coauthors=ignored (|author=suggested) (help) - ^ Liu, K (2013 Sep 1). "Linc2GO: a human LincRNA function annotation resource based on ceRNA hypothesis". Bioinformatics (Oxford, England). 29 (17): 2221–2. PMID 23793747.
{{cite journal}}: Check date values in:|date=(help); Unknown parameter|coauthors=ignored (|author=suggested) (help) - ^ Sumazin, P (2011 Oct 14). "An extensive microRNA-mediated network of RNA-RNA interactions regulates established oncogenic pathways in glioblastoma". Cell. 147 (2): 370–81. PMID 22000015.
{{cite journal}}: Check date values in:|date=(help); Unknown parameter|coauthors=ignored (|author=suggested) (help)