1 Database Overview
Dormanomics Database is a comprehensive multi-omics database dedicated to dormant animals, integrating six omics layers - DNA, RNA, EPT, PRT, MET, and MIC - across dormant species. This platform provides researchers with powerful tools for data exploration, visualization, and analysis.
Genomics (DNA)
Genome assemblies, annotations, and sequence data for dormant species
Transcriptomics (RNA)
Gene expression profiles across dormancy 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 dormancy
Microbiomics (MIC)
Gut and tissue microbiome composition and function during dormancy
Use the search bar in the header for quick keyword search across all database modules.
2 SRA Database
The SRA Database module provides a comprehensive multi-omics raw sequencing data repository for dormancy. It currently hosts 156,030 SRA runs covering six major omics types across dormant species, with interactive search, filtering, and species data matrix browsing.
- Navigate to the Database page from the top navigation bar.
- Browse by Omics Type: Click one of the six data type cards (Genomics, Transcriptomics, Epigenomics, Proteomics, Metabolomics, Microbiomics) to explore relevant SRA entries.
- Species Data Matrix: Use the interactive matrix to filter by taxonomy class (Mammalia, Aves, Reptilia, Amphibia, Insecta, Gastropoda) and view all available data types per species.
- Search: Enter an SRA ID, species name, or keyword in the search box to find specific datasets.
- Species pages: Click any species name to view its dedicated page with omics data summary and external database links.
| Data Type | Content | Typical Assays |
|---|---|---|
| Genomics (DNA) | Whole genome sequencing, resequencing, population genomics | WGS, WES, Resequencing |
| Transcriptomics (RNA) | Gene expression, isoform sequencing, single-cell transcriptomics | RNA-seq, scRNA-seq, Iso-seq |
| Epigenomics (EPT) | DNA methylation, histone modifications, chromatin accessibility | ChIP-seq, ATAC-seq, BS-seq |
| Proteomics (PRT) | Mass spectrometry-based protein identification and quantification | LC-MS/MS, DIA, PTM |
| Metabolomics (MET) | Metabolite profiling during dormancy | LC-MS, GC-MS, NMR |
| Microbiomics (MIC) | Microbiome composition and function from host-associated samples | 16S rRNA, Metagenome, Shotgun |
Use the species data matrix to quickly identify which omics data types are available for a given species. Darker cells indicate more data availability.
3 Genome Browser (JBrowse)
JBrowse 2 is an open-source, interactive genome browser integrated into Dormanomics for visualizing genomic features with high performance. It supports real-time exploration of genetic variations, gene expression patterns, and epigenetic modifications associated with dormancy biology.
- Click JBrowse in the top navigation menu.
- Select a reference genome from the species dropdown (e.g., Ursus maritimus, Spermophilus dauricus).
- Navigate using the toolbar: zoom in/out, pan left/right, or search by gene name or coordinate.
- Toggle annotation tracks (GFF3, BAM, BigWig, VCF) on/off from the left panel.
- Compare multiple tracks simultaneously to correlate genomics with transcriptomics or epigenomics data.
Gene Annotations
Browse GFF3 gene models, CDS, and transcript structures
Expression Tracks
Visualize RNA-seq coverage and expression levels as BigWig tracks
Variant Calling
View SNPs, indels, and structural variants from VCF files
Read Alignment
Inspect BAM/CRAM read alignments at single-base resolution
Arrow keys to pan, +/- to zoom, Ctrl+F to search within the current view. Click on any feature to open the detail popup panel.
4 Analysis Tools
Dormanomics provides 18 online analysis tools for multi-omics data visualization and statistical analysis. Each tool supports demo data for quick testing and generates publication-ready figures. No programming experience is required.
Expression & Differential Analysis
Heatmap
Expression heatmap with hierarchical clustering, annotation tracks, and PDF export
Volcano Plot
Differential expression visualization with fold change and significance thresholds
Boxplot
Group-wise expression comparison with statistical significance markers
Violin Plot
Distribution density plots for expression data across groups
Line Plot
Trend visualization for time-series or dose-response experiments
GSEA Plot
Gene set enrichment analysis curve visualization for pathway analysis
Dimensionality Reduction & Clustering
PCoA
Principal coordinate analysis for beta-diversity visualization
Scatter Plot
2D/3D scatter plots with grouping and regression line options
Phylogenetic Tree
Interactive tree visualization with layout and style customization
Relationship & Composition
Venn Diagram
Compare gene lists and identify overlaps across up to 5 sets
Chord Diagram
Circos-style relationship visualization between categories
Sankey Plot
Flow diagrams showing category transitions and distributions
Radar Chart
Multi-dimensional data comparison across variables
Specialized Visualizations
Fish Plot
Clonal evolution visualization for lineage tracing
Waterfall Plot
Ordered bar plots for mutation or response data
Correlation
Correlation matrix and network visualization
Most tools support demo data for quick testing. Click "Run with Example Data" to see the output format. For your own data, prepare tab-delimited text files following the format templates provided in each tool.
5 Data Download
The Download Center provides a guide and batch download tools for processed multi-omics data. It aggregates resources from major public archives including NCBI Assembly, GEO, PRIDE, BioProject, and GSA/CNGBdb.
- Go to the Download page from the navigation bar.
- Explore the archive cards: Genome Assemblies (NCBI RefSeq), GEO Datasets (expression matrices), PRIDE Proteomics (protein identifications), BioProjects (multi-omics portals), and GSA/CNGB (China National Genomics).
- Click on any archive card to view its description and external link.
- For batch downloads, use the command-line scripts provided in the SRA Toolkit section.
| Archive | Data Type | Content |
|---|---|---|
| NCBI Assembly / RefSeq | Genome | Reference genomes, gene annotations (GFF3/GTF), protein and CDS sequences |
| GEO | Transcriptome | Normalized expression matrices, platform annotations |
| PRIDE | Proteome | Protein identifications (mzIdentML), quantification results |
| BioProject + SRA | Multi-omics | All associated data types with Run Selector for batch download |
| GSA / CNGBdb | Multi-omics | Chinese datasets with CRA/PRJCA accessions |
Most processed data (gene annotations, expression matrices, protein identifications) is ready for immediate analysis. For raw reads (FASTQ), bioinformatics pipelines are required. Check the archive-specific instructions in the Download Center.
6 Q&A AI Assistant
The Q&A AI module (accessible from the bottom-right corner on every page) provides an intelligent assistant to help answer questions about dormancy biology, database usage, and data interpretation.
- Click the AI icon in the bottom-right corner of any page.
- Type your question in the chat input box (supports English and Chinese).
- The AI searches the database knowledge base and provides contextual answers with cited references.
- Click on cited references to view the source data or publications.
The AI assistant provides informational guidance only. For research-critical decisions, please verify with primary literature and domain experts.
7 ScholarGraph (Knowledge Graph)
ScholarGraph integrates ~30,000 dormancy-related publications, featuring interactive keyword co-occurrence, author collaboration, and literature-dataset association networks with PubMed/DOI links.
- Click ScholarGraph in the top navigation menu.
- Search by title, author, or keyword in the search box.
- Explore three network types:
- Keyword Co-occurrence: Discover research hotspots and trending topics in dormancy biology
- Author Collaboration: Identify key researchers and collaboration networks
- Literature-Data: Explore connections between publications and omics datasets
- Click any node to view related publications in the panel below the graph.
- Drag to pan, scroll to zoom, and hover for node details.
Use the graph to identify research gaps by looking for sparsely connected keywords, or find potential collaborators through author network analysis.
8 DormanInsight (AI Engine)
DormanInsight is an academic inspiration engine that generates AI-powered research hypotheses by cross-analyzing multi-omics data and dormancy literature. Select a species and analysis dimensions to receive tailored insights.
- Select a species from the dropdown list.
- Choose analysis dimensions: any combination of six omics types (DNA, RNA, EPT, PRT, MET, MIC) plus AI x Omics integration.
- Click Generate Insights to receive AI-powered hypotheses.
- Review the generated report including:
- Research gaps identified from literature analysis
- Multi-omics cross-domain insights
- AI-generated hypotheses with supporting evidence
Multi-Omics Integration
Cross-analyze up to 6 omics layers simultaneously
Hypothesis Generation
AI-generated research hypotheses with literature support
Research Gap Analysis
Identify under-explored areas in dormancy research
DormanInsight provides AI-generated hypotheses for research inspiration only. All findings should be validated through experimental data and peer-reviewed literature.
9 Frequently Asked Questions
Q: How many species are included in the database?
A: Dormanomics covers dormant species across Mammalia, Aves, Reptilia, Amphibia, Insecta, and Gastropoda, with a total of 131 species in the taxonomy tree.
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 dormancy-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: Dormanomics 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.