1 Database Overview
Hibernomics Database is a comprehensive multi-omics database dedicated to hibernating animals, integrating six omics layers - DNA, RNA, EPT, PRT, MET, and MIC - across 59 hibernating species. This platform provides researchers with powerful tools for data exploration, visualization, and analysis.
Genomics (DNA)
Genome assemblies, annotations, and sequence data for hibernating species
Transcriptomics (RNA)
Gene expression profiles across hibernation stages and tissues
Epigenomics (EPT)
ATAC-seq, ChIP-seq, DNA methylation, and epigenetic regulatory data
Proteomics (PRT)
Protein expression and post-translational modification data
Metabolomics (MET)
Metabolite profiles and pathway analysis during hibernation
Microbiomics (MIC)
Gut and tissue microbiome composition and function during hibernation
Use the search bar in the header for quick keyword search across all database modules.
2 Browsing SRA Database
The SRA Database module allows you to browse and search multi-omics data organized by species and data type. Follow these steps:
- Navigate to the SRA Database page from the top navigation bar.
- Select a species from the taxonomic tree or species list (59 species available).
- Choose data type: Genomics (DNA), Transcriptomics (RNA), Epigenomics (EPT), Proteomics (PRT), Metabolomics (MET), or Microbiomics (MIC).
- Filter results using the search box or tissue/condition filters.
- Click on any accession number to view detailed sample information.
| Data Type | Content | Source |
|---|---|---|
| Genomics (DNA) | Genome assemblies, resequencing data | NCBI, CNGB |
| Transcriptomics (RNA) | RNA-seq, single-cell RNA-seq | NCBI GEO, GSA |
| Epigenomics (EPT) | ATAC-seq, ChIP-seq, DNA methylation | NCBI GEO, GSA |
| Proteomics (PRT) | Protein expression, MS data | iProX, PRIDE |
| Metabolomics (MET) | Metabolite profiling data | MetaboLights, MW |
| Microbiomics (MIC) | 16S rRNA, metagenomics, microbiome | NCBI SRA, ENA |
Some external links require access to the respective databases (NCBI, CNGB, etc.). Ensure you have a stable internet connection.
3 Using the Genome Browser (JBrowse)
JBrowse is an interactive genome browser embedded in Hibernomics for visualizing genomic features. To use JBrowse:
- Click JBrowse in the top navigation menu.
- Select a reference genome from the dropdown (e.g., Ursus maritimus).
- Navigate using the toolbar: zoom in/out, pan left/right, or search by gene name.
- Toggle annotation tracks on/off from the left panel.
- Click on any feature to view detailed information in the popup panel.
Arrow keys to pan, +/- to zoom, Ctrl+F to search within the current view.
4 Analysis Tools
Hibernomics provides a suite of online analysis tools for multi-omics data visualization and exploration. No programming experience is required.
PCA / 3D-PCA
Principal component analysis for dimensionality reduction and sample clustering
Volcano Plot
Visualize differentially expressed genes with fold change and significance
Heatmap
Expression heatmap with hierarchical clustering for gene sets
Venn Diagram
Compare gene lists and identify overlaps across multiple sets
GSEA Plot
Gene set enrichment analysis curve visualization
Boxplot / Violin
Distribution visualization for gene expression across groups
How to use the tools:
- Navigate to Tools from the main menu.
- Select the desired analysis tool from the workflow page or sidebar.
- Upload your data file (supported formats: CSV, TSV, TXT) or use example data.
- Configure parameters (e.g., color scheme, clustering method, P-value threshold).
- Click Generate to create the visualization.
- Download the figure in PNG/SVG/PDF format using the download button.
5 Downloading Data
The Download Center provides access to processed multi-omics datasets and batch download instructions.
- Go to the Download page from the navigation bar.
- Choose the data category: Genome (DNA), Transcriptome (RNA), Epigenome (EPT), Proteome (PRT), Metabolome (MET), or Microbiome (MIC).
- Click on the download link for the dataset you need.
- For batch downloads, use the provided command-line scripts with your accession list.
For large-scale downloads, we recommend using the Amazon S3 or Aspera high-speed transfer protocol. Links are provided in the Download Center.
6 Q&A AI Assistant
The Q&A AI module provides an intelligent assistant to help answer questions about hibernation biology, database usage, and data interpretation.
- Click Q&A AI in the top navigation bar.
- Type your question in the chat input box (supports English and Chinese).
- The AI will search the database knowledge base and provide a contextual answer.
- Click on cited references to view the source data.
The AI assistant provides informational guidance only. For research-critical decisions, please verify with primary literature and domain experts.
7 Frequently Asked Questions
Q: How many species are included in the database?
A: Currently, Hibernomics covers 59 hibernating species across mammals, birds, reptiles, amphibians, fish, and insects.
Q: Is the database free for academic use?
A: Yes, all data and tools are freely available for academic research. Please cite our database in your publications.
Q: Can I submit my own hibernation-related data?
A: We welcome data contributions. Please contact Prof. Zhengrong Yuan at zryuan@bjfu.edu.cn for data submission guidelines.
Q: What browsers are supported?
A: Hibernomics is optimized for Chrome, Firefox, Safari, and Edge (latest versions). Internet Explorer is not supported.
Q: How do I report a bug or request a feature?
A: Please send an email to zryuan@bjfu.edu.cn with a description of the issue or feature request.
Q: Are there any API endpoints available?
A: RESTful API access is planned for future releases. Stay tuned for updates on the homepage announcement section.