Comprehensive reconstruction and visualization of non-coding regulatory networks in human

TY - JOUR

T1 - Comprehensive reconstruction and visualization of non-coding regulatory networks in human

AU - Bonnici, Vincenzo

AU - Russo, Francesco

AU - Bombieri, Nicola

AU - Pulvirenti, Alfredo

AU - Giugno, Rosalba

PY - 2014/1/1

Y1 - 2014/1/1

N2 - 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.

AB - 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.

KW - Cytoscape

KW - Gene expression

KW - LncRNAs

KW - MicroRNAs

KW - Networks

KW - Non-coding RNAs

UR - http://www.scopus.com/inward/record.url?scp=84934922535&partnerID=8YFLogxK

U2 - 10.3389/fbioe.2014.00069

DO - 10.3389/fbioe.2014.00069

M3 - Journal article

AN - SCOPUS:84934922535

SN - 2296-4185

VL - 2

JO - Frontiers in Bioengineering and Biotechnology

JF - Frontiers in Bioengineering and Biotechnology

IS - DEC

M1 - 69

ER -