Combining results from distinct microRNA target prediction tools enhances the performance of analyses
Autor(a) principal: | |
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Data de Publicação: | 2017 |
Outros Autores: | , , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Institucional da UNESP |
Texto Completo: | http://dx.doi.org/10.3389/fgene.2017.00059 http://hdl.handle.net/11449/174667 |
Resumo: | Target prediction is generally the first step toward recognition of bona fide microRNA (miRNA)-target interactions in living cells. Several target prediction tools are now available, which use distinct criteria and stringency to provide the best set of candidate targets for a single miRNA or a subset of miRNAs. However, there are many false-negative predictions, and consensus about the optimum strategy to select and use the output information provided by the target prediction tools is lacking. We compared the performance of four tools cited in literature-TargetScan (TS), miRanda-mirSVR (MR), Pita, and RNA22 (R22), and we determined the most effective approach for analyzing target prediction data (individual, union, or intersection). For this purpose, we calculated the sensitivity, specificity, precision, and correlation of these approaches using 10 miRNAs (miR-1-3p, miR-17-5p, miR-21-5p, miR-24-3p, miR-29a-3p, miR-34a-5p, miR-124-3p, miR-125b-5p, miR-145-5p, and miR-155-5p) and 1,400 genes (700 validated and 700 non-validated) as targets of these miRNAs. The four tools provided a subset of high-quality predictions and returned few false-positive predictions; however, they could not identify several known true targets. We demonstrate that union of TS/MR and TS/MR/R22 enhanced the quality of in silico prediction analysis of miRNA targets. We conclude that the union rather than the intersection of the aforementioned tools is the best strategy for maximizing performance while minimizing the loss of time and resources in subsequent in vivo and in vitro experiments for functional validation of miRNA-target interactions. |
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Repositório Institucional da UNESP |
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Combining results from distinct microRNA target prediction tools enhances the performance of analysesBioinformaticsIn silico predictionMiRanda-mirSVRNon-coding RNAPitaRNA22TargetScanTarget prediction is generally the first step toward recognition of bona fide microRNA (miRNA)-target interactions in living cells. Several target prediction tools are now available, which use distinct criteria and stringency to provide the best set of candidate targets for a single miRNA or a subset of miRNAs. However, there are many false-negative predictions, and consensus about the optimum strategy to select and use the output information provided by the target prediction tools is lacking. We compared the performance of four tools cited in literature-TargetScan (TS), miRanda-mirSVR (MR), Pita, and RNA22 (R22), and we determined the most effective approach for analyzing target prediction data (individual, union, or intersection). For this purpose, we calculated the sensitivity, specificity, precision, and correlation of these approaches using 10 miRNAs (miR-1-3p, miR-17-5p, miR-21-5p, miR-24-3p, miR-29a-3p, miR-34a-5p, miR-124-3p, miR-125b-5p, miR-145-5p, and miR-155-5p) and 1,400 genes (700 validated and 700 non-validated) as targets of these miRNAs. The four tools provided a subset of high-quality predictions and returned few false-positive predictions; however, they could not identify several known true targets. We demonstrate that union of TS/MR and TS/MR/R22 enhanced the quality of in silico prediction analysis of miRNA targets. We conclude that the union rather than the intersection of the aforementioned tools is the best strategy for maximizing performance while minimizing the loss of time and resources in subsequent in vivo and in vitro experiments for functional validation of miRNA-target interactions.Laboratory of Genomics and Molecular Evolution Department of Genetics Institute of Biosciences of Botucatu São Paulo State Univesity (UNESP)Laboratory of Bioinformatics and Computational Biophysics Department of Physics and Biophysics Institute of Biosciences of Botucatu São Paulo State Univesity (UNESP)Laboratory of Genomics and Molecular Evolution Department of Genetics Institute of Biosciences of Botucatu São Paulo State Univesity (UNESP)Laboratory of Bioinformatics and Computational Biophysics Department of Physics and Biophysics Institute of Biosciences of Botucatu São Paulo State Univesity (UNESP)Universidade Estadual Paulista (Unesp)Oliveira, Arthur C. [UNESP]Bovolenta, Luiz A. [UNESP]Nachtigall, Pedro G. [UNESP]Herkenhoff, Marcos E. [UNESP]Lemke, Ney [UNESP]Pinhal, Danillo [UNESP]2018-12-11T17:12:20Z2018-12-11T17:12:20Z2017-05-09info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleapplication/pdfhttp://dx.doi.org/10.3389/fgene.2017.00059Frontiers in Genetics, v. 8, n. MAY, 2017.1664-8021http://hdl.handle.net/11449/17466710.3389/fgene.2017.000592-s2.0-850199362072-s2.0-85019936207.pdf7977035910952141Scopusreponame:Repositório Institucional da UNESPinstname:Universidade Estadual Paulista (UNESP)instacron:UNESPengFrontiers in Genetics2,274info:eu-repo/semantics/openAccess2023-10-04T06:06:14Zoai:repositorio.unesp.br:11449/174667Repositório InstitucionalPUBhttp://repositorio.unesp.br/oai/requestopendoar:29462024-08-05T13:59:25.866957Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)false |
dc.title.none.fl_str_mv |
Combining results from distinct microRNA target prediction tools enhances the performance of analyses |
title |
Combining results from distinct microRNA target prediction tools enhances the performance of analyses |
spellingShingle |
Combining results from distinct microRNA target prediction tools enhances the performance of analyses Oliveira, Arthur C. [UNESP] Bioinformatics In silico prediction MiRanda-mirSVR Non-coding RNA Pita RNA22 TargetScan |
title_short |
Combining results from distinct microRNA target prediction tools enhances the performance of analyses |
title_full |
Combining results from distinct microRNA target prediction tools enhances the performance of analyses |
title_fullStr |
Combining results from distinct microRNA target prediction tools enhances the performance of analyses |
title_full_unstemmed |
Combining results from distinct microRNA target prediction tools enhances the performance of analyses |
title_sort |
Combining results from distinct microRNA target prediction tools enhances the performance of analyses |
author |
Oliveira, Arthur C. [UNESP] |
author_facet |
Oliveira, Arthur C. [UNESP] Bovolenta, Luiz A. [UNESP] Nachtigall, Pedro G. [UNESP] Herkenhoff, Marcos E. [UNESP] Lemke, Ney [UNESP] Pinhal, Danillo [UNESP] |
author_role |
author |
author2 |
Bovolenta, Luiz A. [UNESP] Nachtigall, Pedro G. [UNESP] Herkenhoff, Marcos E. [UNESP] Lemke, Ney [UNESP] Pinhal, Danillo [UNESP] |
author2_role |
author author author author author |
dc.contributor.none.fl_str_mv |
Universidade Estadual Paulista (Unesp) |
dc.contributor.author.fl_str_mv |
Oliveira, Arthur C. [UNESP] Bovolenta, Luiz A. [UNESP] Nachtigall, Pedro G. [UNESP] Herkenhoff, Marcos E. [UNESP] Lemke, Ney [UNESP] Pinhal, Danillo [UNESP] |
dc.subject.por.fl_str_mv |
Bioinformatics In silico prediction MiRanda-mirSVR Non-coding RNA Pita RNA22 TargetScan |
topic |
Bioinformatics In silico prediction MiRanda-mirSVR Non-coding RNA Pita RNA22 TargetScan |
description |
Target prediction is generally the first step toward recognition of bona fide microRNA (miRNA)-target interactions in living cells. Several target prediction tools are now available, which use distinct criteria and stringency to provide the best set of candidate targets for a single miRNA or a subset of miRNAs. However, there are many false-negative predictions, and consensus about the optimum strategy to select and use the output information provided by the target prediction tools is lacking. We compared the performance of four tools cited in literature-TargetScan (TS), miRanda-mirSVR (MR), Pita, and RNA22 (R22), and we determined the most effective approach for analyzing target prediction data (individual, union, or intersection). For this purpose, we calculated the sensitivity, specificity, precision, and correlation of these approaches using 10 miRNAs (miR-1-3p, miR-17-5p, miR-21-5p, miR-24-3p, miR-29a-3p, miR-34a-5p, miR-124-3p, miR-125b-5p, miR-145-5p, and miR-155-5p) and 1,400 genes (700 validated and 700 non-validated) as targets of these miRNAs. The four tools provided a subset of high-quality predictions and returned few false-positive predictions; however, they could not identify several known true targets. We demonstrate that union of TS/MR and TS/MR/R22 enhanced the quality of in silico prediction analysis of miRNA targets. We conclude that the union rather than the intersection of the aforementioned tools is the best strategy for maximizing performance while minimizing the loss of time and resources in subsequent in vivo and in vitro experiments for functional validation of miRNA-target interactions. |
publishDate |
2017 |
dc.date.none.fl_str_mv |
2017-05-09 2018-12-11T17:12:20Z 2018-12-11T17:12:20Z |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/article |
format |
article |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
http://dx.doi.org/10.3389/fgene.2017.00059 Frontiers in Genetics, v. 8, n. MAY, 2017. 1664-8021 http://hdl.handle.net/11449/174667 10.3389/fgene.2017.00059 2-s2.0-85019936207 2-s2.0-85019936207.pdf 7977035910952141 |
url |
http://dx.doi.org/10.3389/fgene.2017.00059 http://hdl.handle.net/11449/174667 |
identifier_str_mv |
Frontiers in Genetics, v. 8, n. MAY, 2017. 1664-8021 10.3389/fgene.2017.00059 2-s2.0-85019936207 2-s2.0-85019936207.pdf 7977035910952141 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
Frontiers in Genetics 2,274 |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
application/pdf |
dc.source.none.fl_str_mv |
Scopus reponame:Repositório Institucional da UNESP instname:Universidade Estadual Paulista (UNESP) instacron:UNESP |
instname_str |
Universidade Estadual Paulista (UNESP) |
instacron_str |
UNESP |
institution |
UNESP |
reponame_str |
Repositório Institucional da UNESP |
collection |
Repositório Institucional da UNESP |
repository.name.fl_str_mv |
Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP) |
repository.mail.fl_str_mv |
|
_version_ |
1808128301588283392 |