GOmir: a stand alone application for human microRNA target analysis and gene ontology clustering

Introduction

MicroRNAs are single-stranded RNA molecules of about 20–23 nucleotides length found in a wide variety of organisms. MicroRNAs regulate gene expression, by interacting with target mRNAs at specific sites in order to induce cleavage of the message or inhibit translation. Predicting or verifying mRNA targets of specific microRNAs is a difficult process of great importance.

GOmir module, JTarget, integrates microRNA target prediction and functional analysis by combining the predicted target genes from TargetScan, miRanda, RNAhybrid and PicTar computational tools and also providing a full gene description and functional analysis for each target gene. In addition, GOmir incorporates TAGGO application, which has been designed to automatically group gene ontology annotations, taking advantage of the Gene Ontology (GO), in order to extract the main attributes of sets of proteins and is available for downloading from http://www.bioacademy.gr/bioinformatics/TAGGO/ .

GOmir (by using up to four different databases) introduces, for the first time, miRNA predicted targets accompanied by (a) full gene description, (b) functional analysis and (c) detailed gene ontology clustering. Additionally, a reverse search initiated by a potential target can also be conducted.

Installation

GOmir is a new stand alone JAVA application for human miRNAs target prediction and ontology clustering, consisting of two different components written in JAVA, JTarget and TAGGO. GOmir can be installed in any operation system with Java Runtime Engine 1.5.0 (JRE 5.0) or above (http://www.java.com/) pre-installed in any Microsoft Windows operation system.

GOmir runs both on Windows and Linux. The user can install GOmir on Windows by running the above setup file or by extracting in his computer the .rar file. There is a .tar.gz file available for Linux. This will install in his/her computer the GOmir application and all the essential data files both for JTarget and TAGGO components. The minimum hard disk space required is 720 MB. After the installation the folder of GOmir will contain two files called “mirnas”, which indicate JTarget microRNAs database, a SQLite dll file, a gene ontology file, a “GOAFiles” properties file, a folder called “GOA files”, which contains gene association files for 7 organisms, an executable Jar file called “GOmir” and a batch file called “Run GOmir”. The user should run GOmir by double clicking on “Run GOmir”.   

User’s Guide

• Target genes for a microRNA from 1 database.

Choose the “Search by microRNA” option and fill the text field with the name of a human microRNA(for example miR-21). Choose which database you want to use by checking one of the five available. Fill optionally the text field “Enter the output file” with the path of the file, where the results are going to be saved. Finally, push the “Find Targets” button. The results will be shown in the central text area.

• Target genes for a microRNA from 2 or more databases.

Choose the “Search by microRNA” option and fill the text field with the name of a human microRNA(for example miR-21). Choose which databases you want to use by checking one of the five available (the user may choose more than one databases). Fill optionally the text field “Enter the output file” with the path of the file, where the results are going to be saved. Finally, push the “Compare databases results” button. The results will be shown in the central text area. A message box informs the user on how many common genes were found in the chosen databases and in how much time this action was performed.

• Target genes for a microRNA from all the databases.

Choose the “Search by microRNA” option and fill the text field with the name of a human microRNA(for example miR-21). There is no need for the user to check any databases. Fill optionally the text field “Enter the output file” with the path of the file, where the results are going to be saved. Finally, push the “Compare All” button. The results will be shown in the central text area. The databases used in this procedure are TargetScan, RNAhybrid, miRanda and PicTar-4way. PicTar 5-way was excluded from the calculation of the common target genes at the “Compare All” procedure, because its insertion reduces the common target genes results to a significant degree. A message box informs the user on how many common genes were found in the chosen databases and in how much time this action was performed.

• Find genes description

After one of the previous actions, the central text area will contain the predicted target genes for a microRNA. The user may find the descriptions (as described by DAVID Bioninformatics database) of these genes by clicking the “Find genes description” button. A progress bar appears that indicates the progress of this procedure.

• Find genes functions

Similarly to the previous procedure the user may find the functions (as described by DAVID Bioninformatics database) of the target genes for a microRNA by clicking the “Find genes functions” button.

*Note that for the last two actions the central text area should contain the target genes of a microRNA as resulted by one of the first three actions.

• Find the microRNAs, which are targets to a given gene

Choose the “Search by gene” option and fill the text field with the official symbol of a gene (for example SOX2). Choose which database you want to use by checking one of the five available ones. Fill optionally the text field “Enter the output file” with the path of the file, where the results are going to be saved. Finally, push the “Find microRNAs” button. The results will be shown in the central text area. Searches for common microRNAs from 2 to 5 databases are available as well, by clicking the “Compare databases results” button or the “Compare All” button.

·         Perform a gene ontology clustering

Once a search is completed, a gene ontology clustering may be performed by clicking the “TAGGO” button. The user will be asked to save the result of the search in a file if he/she had not done so beforehand. A temporary file will be created from the output file of a JTarget search and will then be used as an input file for TAGGO search. For more information about TAGGO please refer to  http://www.bioacademy.gr/bioinformatics/TAGGO/ .

Figure I: JTarget main menu

Figure II: The target genes of miR-21 as given by the procedure “Compare All” (4 databases).