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Comprehensive identification of sexually dimorphic genes in diverse cattle tissues using RNA-seq
BACKGROUND: Molecular mechanisms associated with sexual dimorphism in cattle have not been well elucidated. Furthermore, as recent studies have implied that gene expression patterns are highly tissue specific, it is essential to investigate gene expression in a variety of tissues using RNA-seq. Here...
Autores principales: | , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2016
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4728830/ https://www.ncbi.nlm.nih.gov/pubmed/26818975 http://dx.doi.org/10.1186/s12864-016-2400-4 |
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author | Seo, Minseok Caetano-Anolles, Kelsey Rodriguez-Zas, Sandra Ka, Sojeong Jeong, Jin Young Park, Sungkwon Kim, Min Ji Nho, Whan-Gook Cho, Seoae Kim, Heebal Lee, Hyun-Jeong |
author_facet | Seo, Minseok Caetano-Anolles, Kelsey Rodriguez-Zas, Sandra Ka, Sojeong Jeong, Jin Young Park, Sungkwon Kim, Min Ji Nho, Whan-Gook Cho, Seoae Kim, Heebal Lee, Hyun-Jeong |
author_sort | Seo, Minseok |
collection | PubMed |
description | BACKGROUND: Molecular mechanisms associated with sexual dimorphism in cattle have not been well elucidated. Furthermore, as recent studies have implied that gene expression patterns are highly tissue specific, it is essential to investigate gene expression in a variety of tissues using RNA-seq. Here, we employed and compared two statistical methods, a simple two group test and Analysis of deviance (ANODEV), in order to investigate bovine sexually dimorphic genes in 40 RNA-seq samples distributed across two factors: sex and tissue. RESULTS: As a result, we detected 752 sexually dimorphic genes across tissues from two statistical approaches and identified strong tissue-specific patterns of gene expression. Additionally, significantly detected sex-related genes shared between two mammal species (cattle and rat) were identified using qRT-PCR. CONCLUSIONS: Results of our analyses reveal that sexual dimorphism of metabolic tissues and pituitary gland in cattle involves various biological processes. Several differentially expressed genes between sexes in cattle and rat species are shared, but show tissue-specific patterns. Finally, we concluded that two distinct statistical approaches have their advantages and disadvantages in RNA-seq studies investigating multiple tissues. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-016-2400-4) contains supplementary material, which is available to authorized users. |
format | Online Article Text |
id | pubmed-4728830 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2016 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-47288302016-01-28 Comprehensive identification of sexually dimorphic genes in diverse cattle tissues using RNA-seq Seo, Minseok Caetano-Anolles, Kelsey Rodriguez-Zas, Sandra Ka, Sojeong Jeong, Jin Young Park, Sungkwon Kim, Min Ji Nho, Whan-Gook Cho, Seoae Kim, Heebal Lee, Hyun-Jeong BMC Genomics Research Article BACKGROUND: Molecular mechanisms associated with sexual dimorphism in cattle have not been well elucidated. Furthermore, as recent studies have implied that gene expression patterns are highly tissue specific, it is essential to investigate gene expression in a variety of tissues using RNA-seq. Here, we employed and compared two statistical methods, a simple two group test and Analysis of deviance (ANODEV), in order to investigate bovine sexually dimorphic genes in 40 RNA-seq samples distributed across two factors: sex and tissue. RESULTS: As a result, we detected 752 sexually dimorphic genes across tissues from two statistical approaches and identified strong tissue-specific patterns of gene expression. Additionally, significantly detected sex-related genes shared between two mammal species (cattle and rat) were identified using qRT-PCR. CONCLUSIONS: Results of our analyses reveal that sexual dimorphism of metabolic tissues and pituitary gland in cattle involves various biological processes. Several differentially expressed genes between sexes in cattle and rat species are shared, but show tissue-specific patterns. Finally, we concluded that two distinct statistical approaches have their advantages and disadvantages in RNA-seq studies investigating multiple tissues. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-016-2400-4) contains supplementary material, which is available to authorized users. BioMed Central 2016-01-27 /pmc/articles/PMC4728830/ /pubmed/26818975 http://dx.doi.org/10.1186/s12864-016-2400-4 Text en © Seo et al. 2016 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Research Article Seo, Minseok Caetano-Anolles, Kelsey Rodriguez-Zas, Sandra Ka, Sojeong Jeong, Jin Young Park, Sungkwon Kim, Min Ji Nho, Whan-Gook Cho, Seoae Kim, Heebal Lee, Hyun-Jeong Comprehensive identification of sexually dimorphic genes in diverse cattle tissues using RNA-seq |
title | Comprehensive identification of sexually dimorphic genes in diverse cattle tissues using RNA-seq |
title_full | Comprehensive identification of sexually dimorphic genes in diverse cattle tissues using RNA-seq |
title_fullStr | Comprehensive identification of sexually dimorphic genes in diverse cattle tissues using RNA-seq |
title_full_unstemmed | Comprehensive identification of sexually dimorphic genes in diverse cattle tissues using RNA-seq |
title_short | Comprehensive identification of sexually dimorphic genes in diverse cattle tissues using RNA-seq |
title_sort | comprehensive identification of sexually dimorphic genes in diverse cattle tissues using rna-seq |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4728830/ https://www.ncbi.nlm.nih.gov/pubmed/26818975 http://dx.doi.org/10.1186/s12864-016-2400-4 |
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