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Human microRNA target analysis and gene ontology clustering by GOmir, a novel stand-alone application.

Roubelakis MG, Zotos P, Papachristoudis G, Michalopoulos I, Pappa KI, Anagnou NP, Kossida S - BMC Bioinformatics (2009)

Bottom Line: microRNAs (miRNAs) are single-stranded RNA molecules of about 20-23 nucleotides length found in a wide variety of organisms. miRNAs regulate gene expression, by interacting with target mRNAs at specific sites in order to induce cleavage of the message or inhibit translation.GOmir (by using up to five different databases) introduces miRNA predicted targets accompanied by (a) full gene description, (b) functional analysis and (c) detailed gene ontology clustering.GOmir can freely be downloaded BRFAA.

View Article: PubMed Central - HTML - PubMed

Affiliation: Cell & Gene Therapy Laboratory, Biomedical Research Foundation of the Academy of Athens, Soranou Efesiou 4, 11527, Athens, Greece. mroubelaki@bioacademy.gr

ABSTRACT

Background: microRNAs (miRNAs) are single-stranded RNA molecules of about 20-23 nucleotides length found in a wide variety of organisms. miRNAs 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 miRNAs is a difficult process of great importance.

Results: GOmir is a novel stand-alone application consisting of two separate tools: JTarget and TAGGO. JTarget integrates miRNA target prediction and functional analysis by combining the predicted target genes from TargetScan, miRanda, RNAhybrid and PicTar computational tools as well as the experimentally supported targets from TarBase and also providing a full gene description and functional analysis for each target gene. On the other hand, TAGGO application is 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. GOmir represents a new tool incorporating two separate Java applications integrated into one stand-alone Java application.

Conclusion: GOmir (by using up to five different databases) introduces 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. GOmir can freely be downloaded BRFAA.

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Computational prediction validation by TarBase. (A) Intersection of each prediction database with TarBase. The total number of common targets between each prediction database and TarBase for all the miRNAs available in TarBase was calculated. (B) The number of predicted targets for miR-21 by each predicting database or combinations of them. Experimentally supported targets for miR-21 are provided by TarBase.
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Figure 2: Computational prediction validation by TarBase. (A) Intersection of each prediction database with TarBase. The total number of common targets between each prediction database and TarBase for all the miRNAs available in TarBase was calculated. (B) The number of predicted targets for miR-21 by each predicting database or combinations of them. Experimentally supported targets for miR-21 are provided by TarBase.

Mentions: As described in the previous section, TarBase was also inserted in the JTarget comparative module of GOmir. TarBase describes in full detail the experimentally supported targets of 111 miRNAs and also provides information for the nature of the experiments that were conducted to validate these results [13]. In order to understand the features of miRNA targeting and to validate experimentally the bioinformatics prediction, we performed comparative analyses using prediction databases (TargetScan, miRanda, RNAhybrid, PicTar-4 way and PicTar-5 way) and the experimental one, TarBase. An intersection analysis between each prediction database and TarBase was performed by calculating the total number of common targets between each prediction database and TarBase for all the miRNAs available in TarBase (Figure 2A). TargetScan predictions, as documented in Figure 2A, are validated experimentally in a higher rate compared to miRanda, RNAhybrid, PicTar-4 way and PicTar-5 way.


Human microRNA target analysis and gene ontology clustering by GOmir, a novel stand-alone application.

Roubelakis MG, Zotos P, Papachristoudis G, Michalopoulos I, Pappa KI, Anagnou NP, Kossida S - BMC Bioinformatics (2009)

Computational prediction validation by TarBase. (A) Intersection of each prediction database with TarBase. The total number of common targets between each prediction database and TarBase for all the miRNAs available in TarBase was calculated. (B) The number of predicted targets for miR-21 by each predicting database or combinations of them. Experimentally supported targets for miR-21 are provided by TarBase.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2697644&req=5

Figure 2: Computational prediction validation by TarBase. (A) Intersection of each prediction database with TarBase. The total number of common targets between each prediction database and TarBase for all the miRNAs available in TarBase was calculated. (B) The number of predicted targets for miR-21 by each predicting database or combinations of them. Experimentally supported targets for miR-21 are provided by TarBase.
Mentions: As described in the previous section, TarBase was also inserted in the JTarget comparative module of GOmir. TarBase describes in full detail the experimentally supported targets of 111 miRNAs and also provides information for the nature of the experiments that were conducted to validate these results [13]. In order to understand the features of miRNA targeting and to validate experimentally the bioinformatics prediction, we performed comparative analyses using prediction databases (TargetScan, miRanda, RNAhybrid, PicTar-4 way and PicTar-5 way) and the experimental one, TarBase. An intersection analysis between each prediction database and TarBase was performed by calculating the total number of common targets between each prediction database and TarBase for all the miRNAs available in TarBase (Figure 2A). TargetScan predictions, as documented in Figure 2A, are validated experimentally in a higher rate compared to miRanda, RNAhybrid, PicTar-4 way and PicTar-5 way.

Bottom Line: microRNAs (miRNAs) are single-stranded RNA molecules of about 20-23 nucleotides length found in a wide variety of organisms. miRNAs regulate gene expression, by interacting with target mRNAs at specific sites in order to induce cleavage of the message or inhibit translation.GOmir (by using up to five different databases) introduces miRNA predicted targets accompanied by (a) full gene description, (b) functional analysis and (c) detailed gene ontology clustering.GOmir can freely be downloaded BRFAA.

View Article: PubMed Central - HTML - PubMed

Affiliation: Cell & Gene Therapy Laboratory, Biomedical Research Foundation of the Academy of Athens, Soranou Efesiou 4, 11527, Athens, Greece. mroubelaki@bioacademy.gr

ABSTRACT

Background: microRNAs (miRNAs) are single-stranded RNA molecules of about 20-23 nucleotides length found in a wide variety of organisms. miRNAs 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 miRNAs is a difficult process of great importance.

Results: GOmir is a novel stand-alone application consisting of two separate tools: JTarget and TAGGO. JTarget integrates miRNA target prediction and functional analysis by combining the predicted target genes from TargetScan, miRanda, RNAhybrid and PicTar computational tools as well as the experimentally supported targets from TarBase and also providing a full gene description and functional analysis for each target gene. On the other hand, TAGGO application is 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. GOmir represents a new tool incorporating two separate Java applications integrated into one stand-alone Java application.

Conclusion: GOmir (by using up to five different databases) introduces 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. GOmir can freely be downloaded BRFAA.

Show MeSH