CeRNA database
Competing endogenous RNAs (ceRNAs, also refer as miRNA sponges ) hypothesiss: 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.
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 | [3] |
| cefinder | Competing endogenous RNA database: predicted ceRNA candidates from genome. | database | website | [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 | webserver | [5][6] |
| 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 | [7] |
| Linc2GO | a human LincRNA function annotation resource based on ceRNA webserver. | database | website | [8] |
| . | ||||
References
- ^ Salmena, L (2011 Aug 5). "A ceRNA hypothesis: the Rosetta Stone of a hidden RNA language?". Cell. 146 (3): 353–8. PMID 21802130.
{{cite journal}}: Check date values in:|date=(help); Unknown parameter|coauthors=ignored (|author=suggested) (help) - ^ Tay, Y (2014 Jan 16). "The multilayered complexity of ceRNA crosstalk and competition". Nature. 505 (7483): 344–52. PMID 24429633.
{{cite journal}}: Check date values in:|date=(help); 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) - ^ Sarver, AL (2012). "Competing endogenous RNA database". Bioinformation. 8 (15): 731–3. PMID 23055620.
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|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) - ^ 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) - ^ 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)