title: RAIN: RNA-protein Association and Interaction Networks.
abstract: 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: http://rth.dk/resources/rain.
authors.affiliation: 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.
authors.forename: Alexander
authors.initials: A
authors.lastname: Junge
authors.affiliation: 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.
authors.forename: Jan C
authors.initials: JC
authors.lastname: Refsgaard
authors.affiliation: Center for Non-coding RNA in Technology and Health, University of Copenhagen, Copenhagen,, Groennegaardsvej 3, DK-1870 Frederiksberg C, Denmark.|Center for Biological Sequence Analysis, Technical University of Denmark, Kemitorvet, Building 208, DK-2800 Lyngby, Denmark.
authors.forename: Christian
authors.initials: C
authors.lastname: Garde
authors.affiliation: 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.
authors.forename: Xiaoyong
authors.initials: X
authors.lastname: Pan
authors.affiliation: 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.
authors.forename: Alberto
authors.initials: A
authors.lastname: Santos
authors.affiliation: 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.
authors.forename: Ferhat
authors.initials: F
authors.lastname: Alkan
authors.affiliation: 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.
authors.forename: Christian
authors.initials: C
authors.lastname: Anthon
authors.affiliation: Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland.
authors.forename: Christian
authors.initials: C
authors.lastname: von Mering
authors.affiliation: Center for Non-coding RNA in Technology and Health, University of Copenhagen, Copenhagen,, Groennegaardsvej 3, DK-1870 Frederiksberg C, Denmark.|Center for Biological Sequence Analysis, Technical University of Denmark, Kemitorvet, Building 208, DK-2800 Lyngby, Denmark.
authors.forename: Christopher T
authors.initials: CT
authors.lastname: Workman
authors.affiliation: Center for Non-coding RNA in Technology and Health, University of Copenhagen, 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.
authors.forename: Lars Juhl
authors.initials: LJ
authors.lastname: Jensen
authors.affiliation: 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.
authors.forename: Jan
authors.initials: J
authors.lastname: Gorodkin
mesh_terms: D030541:Databases, Genetic; D035683:MicroRNAs / Q000235:genetics / Q000378:metabolism; D016601:RNA-Binding Proteins / Q000235:genetics / Q000378:metabolism; D014584:User-Computer Interface
chemical_list: D035683:MicroRNAs; D016601:RNA-Binding Proteins