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Database (Oxford). 2017 Jan 10;2017. doi: 10.1093/database/baw167. Print 2017.

RAIN: RNA-protein Association and Interaction Networks.

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Center for Non-coding RNA in Technology and Health, University of Copenhagen, Copenhagen,, Groennegaardsvej 3, DK-1870 Frederiksberg C, Denmark.
Department of Veterinary Clinical and Animal Sciences, University of Copenhagen, Groennegaardsvej 3, DK-1870 Frederiksberg C, Denmark.
Disease Systems Biology Program, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Building: 06-2-26, Blegdamsvej 3B, DK-2200 Copenhagen N, Denmark.
Center for Biological Sequence Analysis, Technical University of Denmark, Kemitorvet, Building 208, DK-2800 Lyngby, Denmark.
Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland.

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Protein association networks can be inferred from a range of resources including experimental data, literature mining and computational predictions. These types of evidence are emerging for non-coding RNAs (ncRNAs) as well. However, integration of ncRNAs into protein association networks is challenging due to data heterogeneity. Here, we present a database of ncRNA-RNA and ncRNA-protein interactions and its integration with the STRING database of protein-protein interactions. These ncRNA associations cover four organisms and have been established from curated examples, experimental data, interaction predictions and automatic literature mining. RAIN uses an integrative scoring scheme to assign a confidence score to each interaction. We demonstrate that RAIN outperforms the underlying microRNA-target predictions in inferring ncRNA interactions. RAIN can be operated through an easily accessible web interface and all interaction data can be downloaded.Database URL:

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