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TargetCompare: A web interface to compare simultaneous miRNAs targets.

Moreira FC, Dustan B, Hamoy IG, Ribeiro-Dos-Santos AM, Dos Santos AR - Bioinformation (2014)

Bottom Line: Hence, we describe a web tool (developed using Java programming language and MySQL database server) to analyse multiple targets of pre-selected miRNAs.We cross validated the tool in eight most highly expressed miRNAs in the antrum region of stomach.This helped to identify 43 potential genes that are target of at least six of the referred miRNAs.

View Article: PubMed Central - PubMed

Affiliation: Laboratorio de Genética Humana e Medica, Instituto de Ciências Biológicas, Universidade Federal do Para, Belem, PA, Brasil ; Centro Universitário do Pará - Área de Ciências Exatas e Tecnologia, , Belém, PA, Brasil.

ABSTRACT

Unlabelled: MicroRNAs (miRNAs) are small non-coding nucleotide sequences between 17 and 25 nucleotides in length that primarily function in the regulation of gene expression. A since miRNA has thousand of predict targets in a complex, regulatory cell signaling network. Therefore, it is of interest to study multiple target genes simultaneously. Hence, we describe a web tool (developed using Java programming language and MySQL database server) to analyse multiple targets of pre-selected miRNAs. We cross validated the tool in eight most highly expressed miRNAs in the antrum region of stomach. This helped to identify 43 potential genes that are target of at least six of the referred miRNAs. The developed tool aims to reduce the randomness and increase the chance of selecting strong candidate target genes and miRNAs responsible for playing important roles in the studied tissue.

Availability: http://lghm.ufpa.br/targetcompare.

No MeSH data available.


TargetCompare flowchart.
© Copyright Policy - open-access
Related In: Results  -  Collection


getmorefigures.php?uid=PMC4209372&req=5

Figure 1: TargetCompare flowchart.

Mentions: The Java (http://www.oracle.com/us/technologies/java/)programming language was used for TargetComparedevelopment and it was implemented as shown in Figure 1.The data used to compare putative targets was downloadedfrom three majors miRNA target prediction datasets:microrna.org [3], targetscan.org [4] and PiTa [12]. To associatethe target genes with diseases, the public Genetic AssociationDatabase [13] was used. To manage the data, MySQL DatabaseServer (http://www. mysql. com/) was used. The web tooltargetCompare is freely available at http://www.lghm.ufpa.br/targetcompare.


TargetCompare: A web interface to compare simultaneous miRNAs targets.

Moreira FC, Dustan B, Hamoy IG, Ribeiro-Dos-Santos AM, Dos Santos AR - Bioinformation (2014)

TargetCompare flowchart.
© Copyright Policy - open-access
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC4209372&req=5

Figure 1: TargetCompare flowchart.
Mentions: The Java (http://www.oracle.com/us/technologies/java/)programming language was used for TargetComparedevelopment and it was implemented as shown in Figure 1.The data used to compare putative targets was downloadedfrom three majors miRNA target prediction datasets:microrna.org [3], targetscan.org [4] and PiTa [12]. To associatethe target genes with diseases, the public Genetic AssociationDatabase [13] was used. To manage the data, MySQL DatabaseServer (http://www. mysql. com/) was used. The web tooltargetCompare is freely available at http://www.lghm.ufpa.br/targetcompare.

Bottom Line: Hence, we describe a web tool (developed using Java programming language and MySQL database server) to analyse multiple targets of pre-selected miRNAs.We cross validated the tool in eight most highly expressed miRNAs in the antrum region of stomach.This helped to identify 43 potential genes that are target of at least six of the referred miRNAs.

View Article: PubMed Central - PubMed

Affiliation: Laboratorio de Genética Humana e Medica, Instituto de Ciências Biológicas, Universidade Federal do Para, Belem, PA, Brasil ; Centro Universitário do Pará - Área de Ciências Exatas e Tecnologia, , Belém, PA, Brasil.

ABSTRACT

Unlabelled: MicroRNAs (miRNAs) are small non-coding nucleotide sequences between 17 and 25 nucleotides in length that primarily function in the regulation of gene expression. A since miRNA has thousand of predict targets in a complex, regulatory cell signaling network. Therefore, it is of interest to study multiple target genes simultaneously. Hence, we describe a web tool (developed using Java programming language and MySQL database server) to analyse multiple targets of pre-selected miRNAs. We cross validated the tool in eight most highly expressed miRNAs in the antrum region of stomach. This helped to identify 43 potential genes that are target of at least six of the referred miRNAs. The developed tool aims to reduce the randomness and increase the chance of selecting strong candidate target genes and miRNAs responsible for playing important roles in the studied tissue.

Availability: http://lghm.ufpa.br/targetcompare.

No MeSH data available.