title: Comprehensive reconstruction and visualization of non-coding regulatory networks in human.
abstract: Research attention has been powered to understand the functional roles of non-coding RNAs (ncRNAs). Many studies have demonstrated their deregulation in cancer and other human disorders. ncRNAs are also present in extracellular human body fluids such as serum and plasma, giving them a great potential as non-invasive biomarkers. However, non-coding RNAs have been relatively recently discovered and a comprehensive database including all of them is still missing. Reconstructing and visualizing the network of ncRNAs interactions are important steps to understand their regulatory mechanism in complex systems. This work presents ncRNA-DB, a NoSQL database that integrates ncRNAs data interactions from a large number of well established on-line repositories. The interactions involve RNA, DNA, proteins, and diseases. ncRNA-DB is available at http://ncrnadb.scienze.univr.it/ncrnadb/. It is equipped with three interfaces: web based, command-line, and a Cytoscape app called ncINetView. By accessing only one resource, users can search for ncRNAs and their interactions, build a network annotated with all known ncRNAs and associated diseases, and use all visual and mining features available in Cytoscape.
authors.affiliation: Department of Computer Science, University of Verona , Verona , Italy.
authors.forename: Vincenzo
authors.initials: V
authors.lastname: Bonnici
authors.affiliation: Laboratory of Integrative Systems Medicine (LISM), Institute of Informatics and Telematics (IIT) and Institute of Clinical Physiology (IFC), National Research Council (CNR) , Pisa , Italy ; Department of Computer Science, University of Pisa , Pisa , Italy.
authors.forename: Francesco
authors.initials: F
authors.lastname: Russo
authors.affiliation: Department of Computer Science, University of Verona , Verona , Italy.
authors.forename: Nicola
authors.initials: N
authors.lastname: Bombieri
authors.affiliation: Department of Clinical and Experimental Medicine, University of Catania , Catania , Italy.
authors.forename: Alfredo
authors.initials: A
authors.lastname: Pulvirenti
authors.affiliation: Department of Clinical and Experimental Medicine, University of Catania , Catania , Italy.
authors.forename: Rosalba
authors.initials: R
authors.lastname: Giugno
keywords: cytoscape; gene expression; lncRNAs; microRNAs; networks; non-coding RNAs