Key Takeaways & Executive Findings
- •• GametesOmics is a comprehensive multi-omics database integrating gene expression, DNA methylation, and chromatin accessibility data for gametogenesis in humans and mice. • The database provides user-friendly tools for gene query, differential expression analysis, correlation analysis, visualization of single-cell clusters, and methylation viewing. • It includes genome browser and ortholog features for cross-species comparison, facilitating the study of germ cell development. • This resource aims to support biologists and clinicians in deciphering the molecular mechanisms underlying oogenesis and spermatogenesis.
Abstract
Gametogenesis plays an important role in the reproduction and evolution of species. The transcriptomic and epigenetic alterations in this process can influence the reproductive capacity, fertilization, and embryonic development. The rapidly increasing single-cell studies have provided valuable multi-omics resources. However, data from different layers and sequencing platforms have not been uniformed and integrated, which greatly limits their use for exploring the molecular mechanisms that underlie oogenesis and spermatogenesis. Here, we develop GametesOmics, a comprehensive database that integrates the data of gene expression, DNA methylation, and chromatin accessibility during oogenesis and spermatogenesis in humans and mice. GametesOmics provides a user-friendly website and various tools, including Search and Advanced Search for querying the expression and epigenetic modification(s) of each gene; Tools with Differentially expressed gene (DEG) analysis for identifying DEGs, Correlation analysis for demonstrating the genetic and epigenetic changes, Visualization for displaying single-cell clusters and screening marker genes as well as master transcription factors (TFs), and MethylView for studying the genomic distribution of epigenetic modifications. GametesOmics also provides Genome Browser and Ortholog for tracking and comparing gene expression, DNA methylation, and chromatin accessibility between humans and mice. GametesOmics offers a comprehensive resource for biologists and clinicians to decipher the cell fate transition in germ cell development, and can be accessed at http://gametesomics.cn/.
1. Introduction
Gametogenesis is a key process in reproduction and evolution of species, during which diploid germ cells undergo mitotic and meiotic divisions, and then differentiate into mature haploid gametes including eggs (oogenesis) and sperms (spermatogenesis) [1,2]. The complex molecular regulatory mechanism involving genetic and epigenetic changes supports the successful genesis of the gametes [3–5]. Nowadays, the rapid development of single-cell sequencing technologies has broadened our understanding of this process and provided a large volume of omics data [6–10]. However, these data have not been integrated or normalized for utilization, which hampers biologists and clinicians to explore the molecular mechanisms that underlie oogenesis as well as spermatogenesis.
Several databases contain valuable omics data of humans and mice. Deeply Integrated Single-Cell Omics data (DISCO) database collects the single-cell RNA sequencing (RNA-seq) datasets covering various tissues and cell types in human, which provides a comprehensive platform for exploring gene expression across different cell types and human tissues [11]. scMethBank database includes DNA methylation data across several species including human and mouse, and provides many useful functions such as search, browsing, and visualization for researchers [12]. dbEmbryo and DevOmics integrate multi-omics sequencing data across different developmental stages in human and mouse early embryos [13,14]. EmAtlas exhibits the spatiotemporal landscape of human and mouse embryos from the perspective of cell, tissue, genome, gene, and protein levels [15]. These current databases greatly promote the understanding of the genetic and epigenetic mechanisms in the development of humans and mice. However, they may lack the collection of comprehensive multi-omics sequencing data of the gametogenesis and online tools for exploring specific stepwise process regarding the oogenesis and spermatogenesis, which may hinder the exploration into the landscape and regulatory mechanisms of the development process during oogenesis and spermatogenesis. Therefore, it is highly desirable to construct a customized database that includes multi-omics data across complete developmental stages and offers user-friendly tools for identifying key regulators of cell fate transition in gametogenesis.
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Jianting An, Jing Wang, Siming Kong, Shi Song, Wei Chen, Peng Yuan, Qilong He, Yidong Chen, Ye Li, Yi Yang, Wei Wang, Rong Li, Liying Yan, Zhiqiang Yan, Jie Qiao (2026). GametesOmics: A Comprehensive Multi-omics Database for Exploring the Gametogenesis in Humans and Mice. Genomics, Proteomics & Bioinformatics. https://doi.org/10.1093/gpb/art_1123
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Frequently Asked Questions
What is GametesOmics?
GametesOmics is a comprehensive multi-omics database that integrates gene expression, DNA methylation, and chromatin accessibility data during oogenesis and spermatogenesis in humans and mice.
What tools does GametesOmics provide?
It provides tools for gene search, differential expression analysis, correlation analysis, visualization of single-cell clusters, marker gene screening, master transcription factor identification, and methylation viewing.
How can GametesOmics help researchers?
It offers a unified platform for exploring the molecular mechanisms underlying gametogenesis, facilitating the identification of key regulators and cross-species comparisons.
Is GametesOmics freely accessible?
Yes, GametesOmics can be accessed at http://gametesomics.cn/.
What species are covered in GametesOmics?
The database covers humans and mice.
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