DoRiNA 2.0—upgrading the doRiNA database of RNA interactions in post-transcriptional regulation

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 esta...

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Bibliographic Details
Published inNucleic acids research Vol. 43; no. D1; pp. D160 - D167
Main Authors Blin, Kai, Dieterich, Christoph, Wurmus, Ricardo, Rajewsky, Nikolaus, Landthaler, Markus, Akalin, Altuna
Format Journal Article
LanguageEnglish
Published England Oxford University Press 28.01.2015
Subjects
Animals
Argonaute Proteins - metabolism
Database Issue
Databases, Genetic
Exons
HEK293 Cells
Humans
Internet
Mice
MicroRNAs - metabolism
Nuclear Proteins - metabolism
RNA - metabolism
RNA Processing, Post-Transcriptional
RNA-Binding Proteins - metabolism
Serine-Arginine Splicing Factors
Software
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Summary: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.
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ISSN:0305-1048
1362-4962
1362-4962
DOI:10.1093/nar/gku1180