Integration and visualization of non-coding RNA and protein interaction networks

Alexander Junge, Jan Christian Refsgaard, Christian Garde, Xiaoyong Pan, Alberto Santos Delgado, Christian Anthon, Ferhat Alkan, Christian von Mering, Christopher Workman, Lars Juhl Jensen, Jan Gorodkin

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    Abstract

    Non-coding RNAs (ncRNAs) fulfill a diverse set of biological functions relying on interactions with other molecular entities. The advent of new experimental and computational approaches makes it possible to study ncRNAs and their associations on an unprecedented scale. We present RAIN (RNA Association and Interaction Networks) - a database that combines ncRNA-ncRNA, ncRNA-mRNA and ncRNA-protein interactions with large-scale protein association networks available in the STRING database. By integrating ncRNA and protein networks, RAIN provides a more complete picture of the cell’s complex interaction network. RAIN aggregates associations and (predicted) interactions of a vast collection of ncRNA classes, including microRNAs and long ncRNAs, collected from a wide range of resources: a) curated knowledge, b) experimentally supported interactions, c) predicted microRNA-target interactions, and d) co-occurrences found by text mining Medline abstracts. Each resource was assigned a reliability score by assessing its agreement with a gold standard set of microRNA-target interactions. RAIN is available at: http://rth.dk/resources/rain
    Original languageEnglish
    Publication date2015
    Number of pages1
    Publication statusPublished - 2015
    EventFirst Annual Danish Bioinformatics Conference - Odense, Denmark
    Duration: 27 Aug 201527 Nov 2015

    Conference

    ConferenceFirst Annual Danish Bioinformatics Conference
    Country/TerritoryDenmark
    CityOdense
    Period27/08/201527/11/2015

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