Limits...
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.

Show MeSH
TAGGO sample analysis. (A) Subcellular destribution of the common target genes for miR-21 as derived from TargetScan and miRanda datasets. (B) Functional classification of the common target genes for miR-21 as derived from TargetScan and miRanda datasets.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC2697644&req=5

Figure 4: TAGGO sample analysis. (A) Subcellular destribution of the common target genes for miR-21 as derived from TargetScan and miRanda datasets. (B) Functional classification of the common target genes for miR-21 as derived from TargetScan and miRanda datasets.

Mentions: Once a search is completed, a gene ontology clustering may be performed by clicking the "TAGGO" button. A temporary file is created from the output file of a JTarget search and is then used as an input file for TAGGO search. TAGGO interface consists of 5 steps (Figure 3). First, the user has to provide the path of the input file containing the proteins. When TAGGO is initiated through JTarget, the first step of TAGGO is done automatically, as the input file is provided directly by JTarget. The second step consists of the selection of the gene ontology file and its format. At the third step, the user is asked to choose the organism for which the clustering is going to be performed. However, for the present analysis the HUMAN checkbox should be selected. The user may then select the Evidence Codes to be included during the annotation process (all of them are included by default), may exclude some non-desired terms or may set a normalised information content threshold for the three aspects. The fifth step is to provide the program with an output directory. The output of the whole process is a directory called "Results", which includes the charts for the visualization of the output, three Venn lists for each GO aspect and some text files with information about the process and its results. For example, according to TAGGO results for the common target genes for miR-21 from TargetScan and miRanda, the most abundant GO term for Cellular Component GO aspect is GO:0005562 which corresponds to intracellular (Figure 4A) and for Molecular Function GO aspect is GO:0005488 which corresponds to binding functions, respectively (Figure 4B). A reverse search is possible to be performed in JTarget, using the "Search by gene" option, in order to find the complementary miRNAs for the given gene. Searches for common miRNAs from 2 to 5 databases are available as well.


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)

TAGGO sample analysis. (A) Subcellular destribution of the common target genes for miR-21 as derived from TargetScan and miRanda datasets. (B) Functional classification of the common target genes for miR-21 as derived from TargetScan and miRanda datasets.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 4: TAGGO sample analysis. (A) Subcellular destribution of the common target genes for miR-21 as derived from TargetScan and miRanda datasets. (B) Functional classification of the common target genes for miR-21 as derived from TargetScan and miRanda datasets.
Mentions: Once a search is completed, a gene ontology clustering may be performed by clicking the "TAGGO" button. A temporary file is created from the output file of a JTarget search and is then used as an input file for TAGGO search. TAGGO interface consists of 5 steps (Figure 3). First, the user has to provide the path of the input file containing the proteins. When TAGGO is initiated through JTarget, the first step of TAGGO is done automatically, as the input file is provided directly by JTarget. The second step consists of the selection of the gene ontology file and its format. At the third step, the user is asked to choose the organism for which the clustering is going to be performed. However, for the present analysis the HUMAN checkbox should be selected. The user may then select the Evidence Codes to be included during the annotation process (all of them are included by default), may exclude some non-desired terms or may set a normalised information content threshold for the three aspects. The fifth step is to provide the program with an output directory. The output of the whole process is a directory called "Results", which includes the charts for the visualization of the output, three Venn lists for each GO aspect and some text files with information about the process and its results. For example, according to TAGGO results for the common target genes for miR-21 from TargetScan and miRanda, the most abundant GO term for Cellular Component GO aspect is GO:0005562 which corresponds to intracellular (Figure 4A) and for Molecular Function GO aspect is GO:0005488 which corresponds to binding functions, respectively (Figure 4B). A reverse search is possible to be performed in JTarget, using the "Search by gene" option, in order to find the complementary miRNAs for the given gene. Searches for common miRNAs from 2 to 5 databases are available as well.

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