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Nucleic acids research2018; 47(D1); D835-D840; doi: 10.1093/nar/gky1040

SAGD: a comprehensive sex-associated gene database from transcriptomes.

Abstract: Many animal species present sex differences. Sex-associated genes (SAGs), which have female-biased or male-biased expression, have major influences on the remarkable sex differences in important traits such as growth, reproduction, disease resistance and behaviors. However, the SAGs resulting in the vast majority of phenotypic sex differences are still unknown. To provide a useful resource for the functional study of SAGs, we manually curated public RNA-seq datasets with paired female and male biological replicates from the same condition and systematically re-analyzed the datasets using standardized methods. We identified 27,793 female-biased SAGs and 64,043 male-biased SAGs from 2,828 samples of 21 species, including human, chimpanzee, macaque, mouse, rat, cow, horse, chicken, zebrafish, seven fly species and five worm species. All these data were cataloged into SAGD, a user-friendly database of SAGs (http://bioinfo.life.hust.edu.cn/SAGD) where users can browse SAGs by gene, species, drug and dataset. In SAGD, the expression, annotation, targeting drugs, homologs, ontology and related RNA-seq datasets of SAGs are provided to help researchers to explore their functions and potential applications in agriculture and human health.
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Publication Date: 2018-11-01 PubMed ID: 30380119PubMed Central: PMC6323940DOI: 10.1093/nar/gky1040Google Scholar: Lookup
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  • Journal Article
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  • Non-U.S. Gov't

Summary

This research summary has been generated with artificial intelligence and may contain errors and omissions. Refer to the original study to confirm details provided. Submit correction.

The research article discusses the creation of a comprehensive database called SAGD, which holds information about Sex-Associated Genes (SAGs). The SAGD holds data about SAGs from 21 species that exhibit sex differences in traits such as growth, reproduction, and disease resistance.

Objective of the Study:

  • The primary goal of this research paper is to curate a vast, comprehensive database featuring Sex-Associated Genes (SAGs) from 21 different animal species. SAGs, which demonstrate either female or male-biased expressions, play a critical role in determining the sex differences in key characteristics such as growth, reproduction, disease resistance, and behaviors.

Methodology:

  • Public RNA sequencing datasets with paired male and female biological replicates undergoing the same conditions were manually curated and systematically re-analyzed using standardized methods.
  • The researchers identified 27,793 female-biased SAGs and 64,043 male-biased SAGs from 2,828 samples spanning 21 species.
  • All this data has been catalogued into the SAGD (Sex-Associated Gene Database). This database is user-friendly, and allows users to explore SAGs by gene, species, drug, and dataset.

Findings and Data Presentation:

  • The SAGD presents the expression, annotation, targeting drugs, homologs, ontology, and linked RNA sequencing datasets of SAGs in a user-friendly interface. This presentation aids researchers in exploring their functions and possible applications in agriculture and human health.
  • The SAGs from multiple species, including humans, chimpanzees, macaques, mice, rats, cows, horses, chickens, zebrafish, seven fly species, and five worm species, showing the broad scope of data included in the database.

Implications and Applications:

  • The creation of this database will allow for better research into SAGs, potentially revealing new findings about sex differences in various species.
  • The findings could have potential applications in agriculture, such as identifying the best animals for breeding or combating diseases, and in human health, such as understanding sex-based differences in disease resistance and responses to medicines.

Cite This Article

APA
Shi MW, Zhang NA, Shi CP, Liu CJ, Luo ZH, Wang DY, Guo AY, Chen ZX. (2018). SAGD: a comprehensive sex-associated gene database from transcriptomes. Nucleic Acids Res, 47(D1), D835-D840. https://doi.org/10.1093/nar/gky1040

Publication

Nucleic acids research
ISSN: 1362-4962
NlmUniqueID: 0411011
Country: England
Language: English
Volume: 47
Issue: D1
Pages: D835-D840

Researcher Affiliations

Shi, Meng-Wei
  • Hubei Key Laboratory of Agricultural Bioinformatics, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China.
Zhang, Na-An
  • Hubei Key Laboratory of Agricultural Bioinformatics, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China.
Shi, Chuan-Ping
  • Hubei Key Laboratory of Agricultural Bioinformatics, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China.
Liu, Chun-Jie
  • Department of Bioinformatics and Systems Biology, Hubei Bioinformatics & Molecular Imaging Key Laboratory, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, PR China.
Luo, Zhi-Hui
  • Hubei Key Laboratory of Agricultural Bioinformatics, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China.
Wang, Dan-Yang
  • Hubei Key Laboratory of Agricultural Bioinformatics, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China.
Guo, An-Yuan
  • Department of Bioinformatics and Systems Biology, Hubei Bioinformatics & Molecular Imaging Key Laboratory, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, PR China.
Chen, Zhen-Xia
  • Hubei Key Laboratory of Agricultural Bioinformatics, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China.

MeSH Terms

  • Animals
  • Cattle
  • Databases, Genetic
  • Diptera / genetics
  • Female
  • Gene Expression Regulation / genetics
  • Horses / genetics
  • Humans
  • Male
  • Mice
  • Molecular Sequence Annotation
  • Rats
  • Reproduction / genetics
  • Sex Characteristics
  • Software
  • Transcriptome / genetics
  • Zebrafish / genetics

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