The DOI matches its Crossref record; 5 of the 5 references it cites were found in a registry or an index.
doRiNA: a database of RNA interactions in post-transcriptional regulation
Open accessAbstract
In animals, RNA binding proteins (RBPs) and microRNAs (miRNAs) post-transcriptionally regulate the expression of virtually all genes by binding to RNA. Recent advances in experimental and computational methods facilitate transcriptome-wide mapping of these interactions. It is thought that the combinatorial action of RBPs and miRNAs on target mRNAs form a post-transcriptional regulatory code. We provide a database that supports the quest for deciphering this regulatory code. Within doRiNA, we are systematically curating, storing and integrating binding site data for RBPs and miRNAs. Users are free to take a target (mRNA) or regulator (RBP and/or miRNA) centric view on the data. We have implemented a database framework with short query response times for complex searches (e.g. asking for all targets of a particular combination of regulators). All search results can be browsed, inspected and analyzed in conjunction with a huge selection of other genome-wide data, because our database is directly linked to a local copy of the UCSC genome browser. At the time of writing, doRiNA encompasses RBP data for the human, mouse and worm genomes. For computational miRNA target site predictions, we provide an update of PicTar predictions.
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Cites
MicroRNAs: Target Recognition and Regulatory Functions
Bartel, D. P. (2009) · Cell · doi:10.1016/j.cell.2009.01.002 · Cited by 20,068
The widespread regulation of microRNA biogenesis, function and decay
Krol, J., Loedige, I., & Filipowicz, W. (2010) · Nature Reviews Genetics · doi:10.1038/nrg2843 · Cited by 4,672
Combinatorial microRNA target predictions
Krek, A., Grün, D., Poy, M. N., Wolf, R., Rosenberg, L., Epstein, E. J., MacMenamin, P., da Piedade, I., Gunsalus, K. C., Stoffel, M., et al. (2005) · Nature Genetics · doi:10.1038/ng1536 · Cited by 4,603
Self-citationHITS-CLIP yields genome-wide insights into brain alternative RNA processing
Licatalosi, D. D., Mele, A., Fak, J. J., Ule, J., Kayikci, M., Chi, S. W., Clark, T. A., Schweitzer, A. C., Blume, J. E., Wang, X., et al. (2008) · Nature · doi:10.1038/nature07488 · Cited by 1,352 · cited 1×
“Additionally, we collect and integrate target sites from published HITS-CLIP experiments (12) and other variants into doRiNA as long as they provide precise positional target site information.”
MethodTranscriptome-wide Analysis of Regulatory Interactions of the RNA-Binding Protein HuR
Lebedeva, S., Jens, M., Theil, K., Schwanhäusser, B., Selbach, M., Landthaler, M., & Rajewsky, N. (2011) · Molecular Cell · doi:10.1016/j.molcel.2011.06.008 · Cited by 716
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Cited by
Predicting effective microRNA target sites in mammalian mRNAs
Agarwal, V., Bell, G. W., Nam, J.-W., & Bartel, D. P. (2015) · eLife · doi:10.7554/elife.05005 · Cited by 7,318
Li, J.-H., Liu, S., Zhou, H., Qu, L.-H., & Yang, J.-H. (2014) · Nucleic Acids Research · doi:10.1093/nar/gkt1248 · Cited by 4,686
Landscape and variation of RNA secondary structure across the human transcriptome
Wan, Y., Qu, K., Zhang, Q. C., Flynn, R. A., Manor, O., Ouyang, Z., Zhang, J., Spitale, R. C., Snyder, M. P., Segal, E., et al. (2014) · Nature · doi:10.1038/nature12946 · Cited by 555
Beck, D., Thoms, J. A. I., Perera, D., Schütte, J., Unnikrishnan, A., Knezevic, K., Kinston, S. J., Wilson, N. K., O’Brien, T. A., Göttgens, B., et al. (2013) · Blood · doi:10.1182/blood-2013-03-490425 · Cited by 133
Metadata
- Authors
- Anders, G., Mackowiak, S. D., Jens, M., Maaskola, J., Kuntzagk, A., Rajewsky, N., Landthaler, M., & Dieterich, C.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2011-11-15
- Volume
- 40
- Issue
- D1
- Pages
- D180-D186
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W2159249646
- Cited by
- 203
- References
- 5
- FWCI
- 8.93
- Type
- journal article
- Language
- en
- Open access
- gold
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- Anders, G., Mackowiak, S. D., Jens, M., Maaskola, J., Kuntzagk, A., Rajewsky, N., Landthaler, M., & Dieterich, C. (2012). doRiNA: a database of RNA interactions in post-transcriptional regulation. Nucleic Acids Research. https://doi.org/10.1093/nar/gkr1007
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