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Meta-Analysis of Oxidative Transcriptomes in Insects
Data accumulation in public databases has resulted in extensive use of meta-analysis, a statistical analysis that combines the results of multiple studies. Oxidative stress occurs when there is an imbalance between free radical activity and antioxidant activity, which can be studied in insects by tr...
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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MDPI
2021
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7996572/ https://www.ncbi.nlm.nih.gov/pubmed/33669076 http://dx.doi.org/10.3390/antiox10030345 |
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author | Bono, Hidemasa |
author_facet | Bono, Hidemasa |
author_sort | Bono, Hidemasa |
collection | PubMed |
description | Data accumulation in public databases has resulted in extensive use of meta-analysis, a statistical analysis that combines the results of multiple studies. Oxidative stress occurs when there is an imbalance between free radical activity and antioxidant activity, which can be studied in insects by transcriptome analysis. This study aimed to apply a meta-analysis approach to evaluate insect oxidative transcriptomes using publicly available data. We collected oxidative stress response-related RNA sequencing (RNA-seq) data for a wide variety of insect species, mainly from public gene expression databases, by manual curation. Only RNA-seq data of Drosophila melanogaster were found and were systematically analyzed using a newly developed RNA-seq analysis workflow for species without a reference genome sequence. The results were evaluated by two metric methods to construct a reference dataset for oxidative stress response studies. Many genes were found to be downregulated under oxidative stress and related to organ system process (GO:0003008) and adherens junction organization (GO:0034332) by gene enrichment analysis. A cross-species analysis was also performed. RNA-seq data of Caenorhabditis elegans were curated, since no RNA-seq data of insect species are currently available in public databases. This method, including the workflow developed, represents a powerful tool for deciphering conserved networks in oxidative stress response. |
format | Online Article Text |
id | pubmed-7996572 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-79965722021-03-27 Meta-Analysis of Oxidative Transcriptomes in Insects Bono, Hidemasa Antioxidants (Basel) Article Data accumulation in public databases has resulted in extensive use of meta-analysis, a statistical analysis that combines the results of multiple studies. Oxidative stress occurs when there is an imbalance between free radical activity and antioxidant activity, which can be studied in insects by transcriptome analysis. This study aimed to apply a meta-analysis approach to evaluate insect oxidative transcriptomes using publicly available data. We collected oxidative stress response-related RNA sequencing (RNA-seq) data for a wide variety of insect species, mainly from public gene expression databases, by manual curation. Only RNA-seq data of Drosophila melanogaster were found and were systematically analyzed using a newly developed RNA-seq analysis workflow for species without a reference genome sequence. The results were evaluated by two metric methods to construct a reference dataset for oxidative stress response studies. Many genes were found to be downregulated under oxidative stress and related to organ system process (GO:0003008) and adherens junction organization (GO:0034332) by gene enrichment analysis. A cross-species analysis was also performed. RNA-seq data of Caenorhabditis elegans were curated, since no RNA-seq data of insect species are currently available in public databases. This method, including the workflow developed, represents a powerful tool for deciphering conserved networks in oxidative stress response. MDPI 2021-02-25 /pmc/articles/PMC7996572/ /pubmed/33669076 http://dx.doi.org/10.3390/antiox10030345 Text en © 2021 by the author. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) ). |
spellingShingle | Article Bono, Hidemasa Meta-Analysis of Oxidative Transcriptomes in Insects |
title | Meta-Analysis of Oxidative Transcriptomes in Insects |
title_full | Meta-Analysis of Oxidative Transcriptomes in Insects |
title_fullStr | Meta-Analysis of Oxidative Transcriptomes in Insects |
title_full_unstemmed | Meta-Analysis of Oxidative Transcriptomes in Insects |
title_short | Meta-Analysis of Oxidative Transcriptomes in Insects |
title_sort | meta-analysis of oxidative transcriptomes in insects |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7996572/ https://www.ncbi.nlm.nih.gov/pubmed/33669076 http://dx.doi.org/10.3390/antiox10030345 |
work_keys_str_mv | AT bonohidemasa metaanalysisofoxidativetranscriptomesininsects |