Human microRNA target analysis and gene ontology clustering by GOmir, a novel stand-alone application
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 o...
| Main Authors: | , , , , , , |
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| Other Authors: | |
| Format: | Article |
| Language: | en_US |
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BioMed Central Ltd.
2009
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| Online Access: | http://hdl.handle.net/1721.1/49470 |
| _version_ | 1811073597038395392 |
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| author | Roubelakis, Maria G. Zotos, Pantelis Papachristoudis, Georgios Michalopoulos, Ioannis Pappa, Kalliopi I. Anagnou, Nicholas P. Kossida, Sophia |
| author2 | Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory |
| author_facet | Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory Roubelakis, Maria G. Zotos, Pantelis Papachristoudis, Georgios Michalopoulos, Ioannis Pappa, Kalliopi I. Anagnou, Nicholas P. Kossida, Sophia |
| author_sort | Roubelakis, Maria G. |
| collection | MIT |
| description | 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. |
| first_indexed | 2024-09-23T09:35:29Z |
| format | Article |
| id | mit-1721.1/49470 |
| institution | Massachusetts Institute of Technology |
| language | en_US |
| last_indexed | 2024-09-23T09:35:29Z |
| publishDate | 2009 |
| publisher | BioMed Central Ltd. |
| record_format | dspace |
| spelling | mit-1721.1/494702022-09-26T12:29:14Z Human microRNA target analysis and gene ontology clustering by GOmir, a novel stand-alone application Roubelakis, Maria G. Zotos, Pantelis Papachristoudis, Georgios Michalopoulos, Ioannis Pappa, Kalliopi I. Anagnou, Nicholas P. Kossida, Sophia Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science Papachristoudis, Georgios Papachristoudis, Georgios 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. 2009-10-19T13:35:29Z 2009-10-19T13:35:29Z 2009-06 Article http://purl.org/eprint/type/JournalArticle 1471-2105 http://hdl.handle.net/1721.1/49470 Roubelakis, Maria, Pantelis Zotos, Georgios Papachristoudis, Ioannis Michalopoulos, Kalliopi Pappa, Nicholas Anagnou, and Sophia Kossida. 2009. Human microRNA target analysis and gene ontology clustering by GOmir, a novel stand-alone application. BMC Bioinformatics 10, no. Suppl 6: S20. 19534746 en_US http://dx.doi.org/10.1186/1471-2105-10-S6-S20 BMC Bioinformatics Creative Commons Attribution http://creativecommons.org/licenses/by/2.0 application/pdf BioMed Central Ltd. Publisher |
| spellingShingle | Roubelakis, Maria G. Zotos, Pantelis Papachristoudis, Georgios Michalopoulos, Ioannis Pappa, Kalliopi I. Anagnou, Nicholas P. Kossida, Sophia Human microRNA target analysis and gene ontology clustering by GOmir, a novel stand-alone application |
| title | Human microRNA target analysis and gene ontology clustering by GOmir, a novel stand-alone application |
| title_full | Human microRNA target analysis and gene ontology clustering by GOmir, a novel stand-alone application |
| title_fullStr | Human microRNA target analysis and gene ontology clustering by GOmir, a novel stand-alone application |
| title_full_unstemmed | Human microRNA target analysis and gene ontology clustering by GOmir, a novel stand-alone application |
| title_short | Human microRNA target analysis and gene ontology clustering by GOmir, a novel stand-alone application |
| title_sort | human microrna target analysis and gene ontology clustering by gomir a novel stand alone application |
| url | http://hdl.handle.net/1721.1/49470 |
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