Limits...
The DIANA-mirExTra web server: from gene expression data to microRNA function.

Alexiou P, Maragkakis M, Papadopoulos GL, Simmosis VA, Zhang L, Hatzigeorgiou AG - PLoS ONE (2010)

Bottom Line: Here, we introduce a user-friendly web-server, DIANA-mirExTra (www.microrna.gr/mirextra) that allows the comparison of frequencies of miRNA associated motifs between sets of genes that can lead to the identification of miRNAs responsible for the deregulation of large numbers of genes.On several datasets of miRNA overexpression and repression experiments, our proposed approaches have successfully identified the deregulated miRNA.Additionally, in case information about miRNA expression changes is provided, the results can be filtered to display the analysis for miRNAs of interest only.

View Article: PubMed Central - PubMed

Affiliation: Biomedical Sciences Research Center "Alexander Fleming", Institute of Molecular Oncology, Varkiza, Greece.

ABSTRACT

Background: High-throughput gene expression experiments are widely used to identify the role of genes involved in biological conditions of interest. MicroRNAs (miRNA) are regulatory molecules that have been functionally associated with several developmental programs and their deregulation with diverse diseases including cancer.

Methodology/principal findings: Although miRNA expression levels may not be routinely measured in high-throughput experiments, a possible involvement of miRNAs in the deregulation of gene expression can be computationally predicted and quantified through analysis of overrepresented motifs in the deregulated genes 3' untranslated region (3'UTR) sequences. Here, we introduce a user-friendly web-server, DIANA-mirExTra (www.microrna.gr/mirextra) that allows the comparison of frequencies of miRNA associated motifs between sets of genes that can lead to the identification of miRNAs responsible for the deregulation of large numbers of genes. To this end, we have investigated different approaches and measures, and have practically implemented them on experimental data.

Conclusions/significance: On several datasets of miRNA overexpression and repression experiments, our proposed approaches have successfully identified the deregulated miRNA. Beyond the prediction of miRNAs responsible for the deregulation of transcripts, the web-server provides extensive links to DIANA-mirPath, a functional analysis tool incorporating miRNA targets in biological pathways. Additionally, in case information about miRNA expression changes is provided, the results can be filtered to display the analysis for miRNAs of interest only.

Show MeSH

Related in: MedlinePlus

Overview of the algorithm.For each possible hexamer, the occurrences on the 3′UTRs of changed and unchanged genes are counted. The counts are compared using the Wilcoxon Rank Sum Test and a p-value produced. The distribution of p-values is plotted in a histogram. Hexamers are mapped back to known miRNA sequences (see Figure 1). When DIANA-microT target prediction scores are used, the Wilcoxon Rank Sum Test is performed between scores of changed and unchanged genes. A p-value is calculated for each miRNA and a corresponding histogram is produced. The histogram and sorted p-values are returned to the user in the Results page (see Figure 4).
© Copyright Policy
Related In: Results  -  Collection


getmorefigures.php?uid=PMC2820085&req=5

pone-0009171-g002: Overview of the algorithm.For each possible hexamer, the occurrences on the 3′UTRs of changed and unchanged genes are counted. The counts are compared using the Wilcoxon Rank Sum Test and a p-value produced. The distribution of p-values is plotted in a histogram. Hexamers are mapped back to known miRNA sequences (see Figure 1). When DIANA-microT target prediction scores are used, the Wilcoxon Rank Sum Test is performed between scores of changed and unchanged genes. A p-value is calculated for each miRNA and a corresponding histogram is produced. The histogram and sorted p-values are returned to the user in the Results page (see Figure 4).

Mentions: The basic analysis flow of DIANA-mirExTra (www.microrna.gr/mirextra) is outlined in Figure 2. In the following section we will discuss each step of the algorithm in detail


The DIANA-mirExTra web server: from gene expression data to microRNA function.

Alexiou P, Maragkakis M, Papadopoulos GL, Simmosis VA, Zhang L, Hatzigeorgiou AG - PLoS ONE (2010)

Overview of the algorithm.For each possible hexamer, the occurrences on the 3′UTRs of changed and unchanged genes are counted. The counts are compared using the Wilcoxon Rank Sum Test and a p-value produced. The distribution of p-values is plotted in a histogram. Hexamers are mapped back to known miRNA sequences (see Figure 1). When DIANA-microT target prediction scores are used, the Wilcoxon Rank Sum Test is performed between scores of changed and unchanged genes. A p-value is calculated for each miRNA and a corresponding histogram is produced. The histogram and sorted p-values are returned to the user in the Results page (see Figure 4).
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2820085&req=5

pone-0009171-g002: Overview of the algorithm.For each possible hexamer, the occurrences on the 3′UTRs of changed and unchanged genes are counted. The counts are compared using the Wilcoxon Rank Sum Test and a p-value produced. The distribution of p-values is plotted in a histogram. Hexamers are mapped back to known miRNA sequences (see Figure 1). When DIANA-microT target prediction scores are used, the Wilcoxon Rank Sum Test is performed between scores of changed and unchanged genes. A p-value is calculated for each miRNA and a corresponding histogram is produced. The histogram and sorted p-values are returned to the user in the Results page (see Figure 4).
Mentions: The basic analysis flow of DIANA-mirExTra (www.microrna.gr/mirextra) is outlined in Figure 2. In the following section we will discuss each step of the algorithm in detail

Bottom Line: Here, we introduce a user-friendly web-server, DIANA-mirExTra (www.microrna.gr/mirextra) that allows the comparison of frequencies of miRNA associated motifs between sets of genes that can lead to the identification of miRNAs responsible for the deregulation of large numbers of genes.On several datasets of miRNA overexpression and repression experiments, our proposed approaches have successfully identified the deregulated miRNA.Additionally, in case information about miRNA expression changes is provided, the results can be filtered to display the analysis for miRNAs of interest only.

View Article: PubMed Central - PubMed

Affiliation: Biomedical Sciences Research Center "Alexander Fleming", Institute of Molecular Oncology, Varkiza, Greece.

ABSTRACT

Background: High-throughput gene expression experiments are widely used to identify the role of genes involved in biological conditions of interest. MicroRNAs (miRNA) are regulatory molecules that have been functionally associated with several developmental programs and their deregulation with diverse diseases including cancer.

Methodology/principal findings: Although miRNA expression levels may not be routinely measured in high-throughput experiments, a possible involvement of miRNAs in the deregulation of gene expression can be computationally predicted and quantified through analysis of overrepresented motifs in the deregulated genes 3' untranslated region (3'UTR) sequences. Here, we introduce a user-friendly web-server, DIANA-mirExTra (www.microrna.gr/mirextra) that allows the comparison of frequencies of miRNA associated motifs between sets of genes that can lead to the identification of miRNAs responsible for the deregulation of large numbers of genes. To this end, we have investigated different approaches and measures, and have practically implemented them on experimental data.

Conclusions/significance: On several datasets of miRNA overexpression and repression experiments, our proposed approaches have successfully identified the deregulated miRNA. Beyond the prediction of miRNAs responsible for the deregulation of transcripts, the web-server provides extensive links to DIANA-mirPath, a functional analysis tool incorporating miRNA targets in biological pathways. Additionally, in case information about miRNA expression changes is provided, the results can be filtered to display the analysis for miRNAs of interest only.

Show MeSH
Related in: MedlinePlus