Welcome to the miRandola tutorial!

If you use miRandola please cite the following Conference Proceedings:Russo,F., Di Bella,S., Nigita,G., Macca,V., Laganà,A., Giugno,R., Pulvirenti,A. andFerro,A. (2012) miRandola: extracellular circulating microRNAs database. EMBnet.journal18 (A), p. 135

IntroductionMicroRNAs are small noncoding RNAs that play an important role in the regulation ofvarious biological processes through their interaction with cellular messenger RNAs. Theyare frequently dysregulated in cancer and have shown great potential as tissue-basedmarkers for cancer classification and prognostication. microRNAs are also present inextracellular human body fluids such as serum, plasma, saliva, and urine and these areoften associated with various pathological conditions including cancer. CirculatingmicroRNAs have been found in membrane-bound vesicles such as exosomes. However,the majority of them are present in human plasma and serum cofractionate with theArgonaute2 (Ago2) protein, rather than with vesicles. Since microRNAs circulate in thebloodstream in a highly stable, extracellular form, they may be used as blood-basedbiomarkers for cancer and other diseases.Therefore, a knowledge base for the storage, classification and analysis of extracellularcirculating miRNA is a fundamental tool for biomedical research. In this work, we presentmiRandola, a comprehensive manually curated classification of extracellular circulatingmiRNAs. To date, the miRandola database contains data obtained from 80 papers, 2089entries, with 576 unique mature miRNAs and 21 types of samples. miRNAs are classifiedinto four categories, based on their extracellular form: miRNA-Ago2, miRNA-exosome,miRNA-HDL and miRNA-circulating. The latter is used when authors don’t distinguishbetween Ago2, exosome or HDL.miRandola is connected to miRò, the miRNA knowledge base, allowing users to infer thepotential biological functions of circulating miRNAs and their connections with phenotype.

Home pageThe Home page provides useful links to our tools:

- miRò is a web-based knowledge base that provides users with miRNA–phenotypeassociations in humans. It integrates data from various online sources, such as databasesof miRNAs, ontologies, diseases and targets, into a unified database equipped with anintuitive and flexible query interface and data mining facilities [Laganà,A., Forte,S.,Giudice,A., Arena,M.R., Puglisi,P.L., Giugno,R., Pulvirenti,A., Shasha,D. and Ferro,A.(2009) miRò: a miRNA knowledge base. Database (Oxford). 2009:bap008].- miRiam is a novel program based on both thermodynamics features and empiricalconstraints, to predict miRNAs/human targets interactions [Laganà,A., Forte,S., Russo,F.,Giugno,R., Pulvirenti,A., Ferro,A. (2010) Prediction of human targets for viral-encodedmicroRNAs by thermodynamics and empirical constraints. J RNAi Gene Silencing. 2010May 24;6(1):379-85].- miRScape is a Cytoscape plugin allowing mining on biological networks annotated withmicroRNAs. It makes use of the knowledge base miRò, which introduce a new layer ofassociations between genes and phenotypes based on miRNAs annotations [Ferro,A.,Giugno,R., Laganà,A., Mongiovì,M., Pigola,G., Pulvirenti,A., Bader,G. and Shasha,D.(2009) miRScape: A Cytoscape Plugin to Annotate Biological Networks with microRNAs.NETTAB 2009].

All the tools are available from http://ferrolab.dmi.unict.it/index.html

Search page

In the Search page, users can select different categories and they can retrieve datathrough simple steps:

Step 1Select category (e.g. Mature miRNA)

Step 2Select mature miRNA (e.g. hsa-let-7a)

Or search mature miRNA through a simple text search (e.g. hsa-let-7a)

Step 3Click on search button. After clicking on search button the database will show the resultstable and the number of results obtained. The results of the queries can also be exportedto various formats such as CSV, XLS and TXT, also to facilitate automatic parsing andanalysis.Users can see data taken from three databases. General information about the miRNAs(Mature miRNA from miRBase, miRBase accession, miRNA family) is obtained frommiRBase while information about the extracellular/circulating miRNAs is obtained fromPubMed (http://www.ncbi.nlm.nih.gov/pubmed/) and ExoCarta [Mathivanan,S.,Fahner,C.J., Reid,G.E., Simpson,R.J. (2012) ExoCarta 2012: database of exosomalproteins, RNA and lipids. Nucleic Acids Res. 40(Database issue):D1241-4].

In order to help formulate hypotheses on the function of secretory miRNAs, we connectedmiRandola to the miRò knowledge base, a web environment which provides users withmiRNA functional annotations inferred through their validated and predicted targets.In particular, each entry in miRandola provides links to the diseases, processes andfunctions in which the corresponding miRNA is involved and the tissues in which it isexpressed. For example after clicking on (F) users will see the miRò results table for hsa-let-7a associated functions:

Advanced Search page

In the Advanced Search page users can select to search among the categories miRNAfamily or mature miRNA.

Step 1Select category (e.g. miRNA family)

Step 2Select miRNA family (e.g. let-7) AND miRNA type (e.g. Ago2) AND/OR sample (e.g.plasma)

Step 3Click on search button. After clicking on search button the database will show the resultstable and the number of results obtained. The results of the queries can also be exportedto various formats such as CSV, XLS and TXT, also to facilitate automatic parsing andanalysis.

Tools pageIn this page, users can use the miRNA Converter tool to convert miRNA IDs to the lastmiRBase version.We have retrieved most of the information from articles published from 2008 to early 2012.The majority of these papers referred to older versions of miRBase [Kozomara,A. andGriffiths-Jones,S. (2011) miRBase: integrating microRNA annotation and deep-sequencingdata. Nucleic Acids Res. 39(Database issue):D152-7]. Moreover, the authors of miRBaserecently reviewed their nomenclature system. These changes in miRNA IDs can affect theidentification and retrieval of the desired data. For this reason, each entry in miRandolacontains both the miRNA ID used in the source paper and the latest miRBase official ID. Inaddition, we have also included a useful online conversion tool which provides, for eachmiRNA, the history of IDs from release 12 of miRBase to release 18.

Users can select miRNA IDs (e.g. hsa-let-7a):

Or they can type miRNA IDs separated by commas (e.g. hsa-let-7a,hsa-let-7b):

After clicking on View button the database will show the results table:

Download/Upload pageAnother important feature that we implemented in miRandola allows users to give theircontribution to the project by submitting new data about extracellular/circulating miRNA.

Users can type one or more mature miRNA IDs but separated by commas (e.g. hsa-let-7a,hsa-miR-106a,hsa-miR-106b):

If authors want to be alerted when we will enter their data in our database they can sendus the email contact and after careful review performed by the miRandola staff, we willupdate our database.Users can download the xls file of the different miRandola versions.

Terminology Used in this tutorial:Ago2: Argonaute 2 proteinExosome: exosomes are 50-nm to 90-nm vesicles arising from multivesicular bodies andreleased by exocytosisHDL: High-density lipoprotein

Comments, questions?Prof. Alfredo FerroUniversità degli Studi di Catania - Dipartimento di Matematica e InformaticaCittà Universitaria - Viale A.Doria, 6 - 95125 Catania - ITALYTel: +39 095383071Fax: +39 0957337032 / +39 095330094E-mail: ferro@dmi.unict.itWebsite: http://www.dmi.unict.it/~ferro