OmicsDB

OmicsDB integrates large-scale genomic and transcriptomic datasets to enable exploration and analysis of functional networks and gene-level information for plant pathogens and selected reference organisms.

Key Features:

• Integrated Omics Data: Contains genomic and transcriptomics data for ten species including Fusarium graminearum, Ustilago maydis, Blumeria graminis, Neurospora crassa, Schizosaccharomyces pombe, Saccharomyces cerevisiae, Escherichia coli, Arabidopsis thaliana, Mus musculus, and Homo sapiens.
• Graph-Based Database Model: Implements a graph-based database structure that supports complex network analysis and flexible querying of biological relationships.
• Analysis Tools: Includes BLAST for sequence alignment, Cytoscape.js for network visualization, and Gene Ontology (GO) enrichment analysis for functional interpretation.
• Data Access: Provides access to ortholog annotations, protein domain information, and publications citing specific genes.

Scientific Applications:

• Molecular mechanism analysis: Enables investigation of molecular mechanisms in plant pathogens through integrated network and expression data.
• In-silico gene discovery: Supports gene discovery across plants, animals, and microbes using integrated genomic and transcriptomic evidence.
• Hypothesis generation: Facilitates generation of hypotheses about gene function and interactions based on co-expression and network context.
• Comparative and evolutionary analysis: Allows exploration of evolutionary relationships and comparative network features across pathogens and reference organisms to identify potential targets for disease control.

Methodology:

Integration of genomic and transcriptomic datasets into a graph-based database that enables dynamic querying and visualization of biological networks, with sequence alignment via BLAST, network rendering via Cytoscape.js, and GO enrichment analysis for functional interpretation.