MaGenDB

MaGenDB provides an integrated functional genomics database for the Malvaceae family (including cotton, cacao, and durian), aggregating genomes, annotations, and processed omics datasets to support comparative genomics and functional analysis.

Key Features:

• Genomic Data Collection: Compiles the genomes of 13 Malvaceae species to support multi-species comparative analyses.
• Comprehensive Annotation: Annotates genes for functional RNA/protein components, Gene Ontology (GO) terms, KEGG orthology, and gene family assignments.
• Omics Data Integration: Processes 374 diverse omics datasets using ENCODE pipelines for integrated analysis.
• Molecular-level Visualization: Provides visual representations of gene-, RNA-, and protein-level data including expression profiles and functional elements.
• Gene Mining: Implements a smart search system for mining genes based on multiple criteria.
• Functional Comparison: Offers a functional comparison system to compare genes across multiple features within a species or between closely related species.

Scientific Applications:

• Comparative Genomics: Enables comparative genomics and evolutionary analyses across the Malvaceae family.
• Trait-related Gene Characterization: Supports functional annotation and characterization of genes linked to agriculturally important traits in cotton, cacao, and durian.
• Expression and Regulatory Analysis: Facilitates identification of gene expression patterns and regulatory elements that contribute to phenotypic diversity.
• Pathway and Gene Discovery: Aids discovery of novel genes and pathways involved in plant development, stress responses, and metabolic processes.

Methodology:

Omics datasets (374 sets) were processed using ENCODE pipelines, and genes were annotated for functional RNA/protein components, Gene Ontology (GO) terms, KEGG orthology, and gene family assignments.