miRandola 2016: the latest version of the circulating RNA database
Creators: name: Russo, Francesco
name: Bella, Sebastiano Di
name: Nigita, Giovanni
name: Vannini, Federica
name: Berti, Gabriele
name: Scoyni, Flavia
name: Laganà, Alessandro
name: Pulvirenti, Alfredo
name: Giugno, Rosalba
name: Pellegrini, Marco
name: Belling, Kirstine
name: Brunak, Søren
name: Ferro, Alfredo
Publisher: name: F1000Research
Year: 2016

description: Non-coding RNAs (ncRNAs) such as for example microRNAs (miRNAs) are frequently dysregulated in cancer and have shown great potential as tissue-based markers for cancer classification and prognostication. ncRNAs are present in membrane-bound vesicles, such as exosomes, in extracellular human body fluids. Circulating miRNAs are also present in human plasma and serum cofractionate with the Argonaute2 (Ago2) protein and the High-density lipoprotein (HDL). Since miRNAs and the other ncRNAs circulate in the bloodstream in a highly stable, extracellular forms, they may be used as blood-based biomarkers for cancer and other diseases. A knowledge base of non-invasive biomarkers is a fundamental tool for biomedical research.<br><br>Data is manually collected from ExoCarta, a database of exosomal proteins, RNA and lipids and PubMed. Articles containing information on circulating RNAs are collected by querying PubMed database using keywords such as “microRNA”, “miRNA”, “extracellular” and “circulating”. Data is then manually extracted from the retrieved papers. General information about miRNAs is obtained from miRBase. The aim of miRandola is to collect data concerning RNAs contained not only in exosomes but in all extracellular types functionally enriched with information such as diseases, processes, functions, associated tissues, and their potential roles as biomarkers.<br><br>Here, we present an updated version of the miRandola database, a comprehensive manually curated collection and classification of extracellular circulating RNAs. The first version of the database has been published in 2012 and it contained 89 papers, 2132 entries and 581 unique mature miRNAs. Now, we have updated the database with 271 papers, 2695 entries, 673 miRNAs and 12 long non-coding RNAs. RNAs are classified into several categories, based on their extracellular form: RNA-Ago2, RNA-exosome, RNA-microvesicles, RNA-HDL and RNA-circulating. Moreover, the database contains several tools, allowing users to infer the potential biological functions of circulating miRNAs, their connections with phenotypes and the drug effects on cellular and extracellular miRNAs.<br><br>miRandola is the first online resource which gathers all the available data on circulating RNAs in a unique environment. It represents a useful reference tool for anyone investigating the role of extracellular RNAs as biomarkers as well as their physiological function and their involvement in pathologies. miRandola is constantly updated (usually once a year) and the online submission system is a crucial feature which helps ensuring that the system is always up-to-date. The future direction of the database is to be a resource for all the potential non-invasive biomarkers such as cell-free DNA, circular RNA and circulating tumor cells (CTCs). miRandola is available online at: http://mirandola.iit.cnr.it/ or http://atlas.dmi.unict.it/mirandola/