DoRiNA


25416797	DoRiNA 2.0--upgrading the doRiNA database of RNA interactions in post-transcriptional regulation. [PMID: 25416797] Blin K, Dieterich C, Wurmus R, Rajewsky N, Landthaler M, Akalin A. Abstract The expression of almost all genes in animals is subject to post-transcriptional regulation by RNA binding proteins (RBPs) and microRNAs (miRNAs). The interactions between both RBPs and miRNAs with mRNA can be mapped on a whole-transcriptome level using experimental and computational techniques established in the past years. The combined action of RBPs and miRNAs is thought to form a post-transcriptional regulatory code. Here we present doRiNA 2.0, available at http://dorina.mdc-berlin.de. In this highly improved new version, we have completely reworked the user interface and expanded the database to improve the usability of the website. Taking into account user feedback over the past years, the input forms for both the simple and the combinatorial search function have been streamlined and combined into a single web page that will also display the search results. Especially, custom uploads is one of the key new features in doRiNA 2.0. To enable the inclusion of doRiNA into third-party analysis pipelines, all operations are accessible via a REST API. Alternatively, local installations can be queried using a Python API. Both the web application and the APIs are available under an OSI-approved Open Source license that allows research and commercial access and re-use. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research. Nucleic Acids Res. 2015:43(Database issue) \| 75 Citations (from Europe PMC, 2025-03-22)
22086949	doRiNA: a database of RNA interactions in post-transcriptional regulation. [PMID: 22086949] Anders G, Mackowiak SD, Jens M, Maaskola J, Kuntzagk A, Rajewsky N, Landthaler M, Dieterich C. Abstract 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. Nucleic Acids Res. 2012:40(Database issue) \| 118 Citations (from Europe PMC, 2025-03-22)

DoRiNA 2.0--upgrading the doRiNA database of RNA interactions in post-transcriptional regulation. [PMID: 25416797]

Blin K, Dieterich C, Wurmus R, Rajewsky N, Landthaler M, Akalin A.

The expression of almost all genes in animals is subject to post-transcriptional regulation by RNA binding proteins (RBPs) and microRNAs (miRNAs). The interactions between both RBPs and miRNAs with mRNA can be mapped on a whole-transcriptome level using experimental and computational techniques established in the past years. The combined action of RBPs and miRNAs is thought to form a post-transcriptional regulatory code. Here we present doRiNA 2.0, available at http://dorina.mdc-berlin.de. In this highly improved new version, we have completely reworked the user interface and expanded the database to improve the usability of the website. Taking into account user feedback over the past years, the input forms for both the simple and the combinatorial search function have been streamlined and combined into a single web page that will also display the search results. Especially, custom uploads is one of the key new features in doRiNA 2.0. To enable the inclusion of doRiNA into third-party analysis pipelines, all operations are accessible via a REST API. Alternatively, local installations can be queried using a Python API. Both the web application and the APIs are available under an OSI-approved Open Source license that allows research and commercial access and re-use. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Nucleic Acids Res. 2015:43(Database issue) | 75 Citations (from Europe PMC, 2025-03-22)

doRiNA: a database of RNA interactions in post-transcriptional regulation. [PMID: 22086949]

Anders G, Mackowiak SD, Jens M, Maaskola J, Kuntzagk A, Rajewsky N, Landthaler M, Dieterich C.

Abstract

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.

Nucleic Acids Res. 2012:40(Database issue) | 118 Citations (from Europe PMC, 2025-03-22)

URL:	http://dorina.mdc-berlin.de/
Full name:	Database of RNA Interactions in Post-transcriptional Regulation
Description:	doRiNA is designed to curate, store and integrate binding site data for RBPs and miRNAs for the human, mouse and worm genomes.
Year founded:	2012
Last update:	NA
Version:	v2.0
Accessibility:	Accessible
Country/Region:	Germany

Data type:	RNA
Data object:	Animal
Database category:	Expression Gene genome and annotation Modification
Major species:	Caenorhabditis elegans Homo sapiens Mus musculus Drosophila melanogaster
Keywords:	miRNA post-transcriptional regulation RNA binding protein

University/Institution:	Max Planck Institute for Biology of Ageing
Address:	Computational RNA Biology Group,Max Planck Institute for Biology of Ageing,50931 Cologne,Germany
City:	Cologne
Province/State:
Country/Region:	Germany
Contact name (PI/Team):	Christoph Dieterich
Contact email (PI/Helpdesk):	christoph.dieterich@age.mpg.de

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Database Commons a catalog of worldwide biological databases