Overview
This database provides integrated gene information, expression profiles, and several analysis tools related to fruit ripening. A key feature of FruitRipGDB is its suite of online analysis tools, including GO/KEGG enrichment, GSEA, and WGCNA. These utilities enable biologists to easily conduct downstream omics data analysis without programming. We are pleased to provide a comprehensive user guide for our database, and we hope that you will find it both informative and enjoyable to use.
What does FruitRipGDB have?
FruitRipGDB mainly provides five modules:
Home - Users can access species-specific gene pages by clicking on the corresponding fruit species images.
Species - Including detailed information for all 30 fruit species included in the database.
Genes - Including a detailed table listing all ripening-related genes for the selected species.
Tools - Online analysis tools including GO/KEGG enrichment, GSEA, and WGCNA.
Expression - Including transcriptome data related to fruit ripening for each fruit species.
Main features of FruitRipGDB
Extensive Gene Repository
Our database houses a vast collection of genes associated with the ripening process in various fruit species, providing a rich source of information for genetic studies.
User-Friendly Interface
Accessible and intuitive, our interface allows users to easily search, sort, and filter genes based on multiple criteria such as species, gene function, and expression patterns.
Integrated Tools
The database is equipped with tools for GO/KEGG enrichment, GSEA, and WGCNA to support comprehensive research projects.
Comprehensive Transcriptomic Insights
Explore differential expression profiles and GO/KEGG enrichment analyses for different fruit species, delivering in-depth, systems-level views of ripening-related gene activity.
Home Module
From the FruitRipGDB homepage, users can access species-specific gene pages by clicking on the corresponding fruit species images.
Species Module
The “Species” module provides detailed information for all 30 fruit species included in the database.
Users can easily explore fruit ripening genes or transcriptome datasets using two buttons.
Genes Module
Users can explore ripening-related genes across various fruit species through either an interactive bar chart or tree view.
Upon selecting a specific fruit species, a word cloud is dynamically generated, highlighting the most frequently reported ripening-related genes for that species.
The “Genes” module also includes a detailed table listing all ripening-related genes for the selected species.
Clicking on a gene name in the table redirects users to a dedicated page containing comprehensive information, including gene name, genomic location, functional annotation, and external links to external resources such as Pfam and UniProt.
Tools Module
The “Tools” module offers several online analysis tools: Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses, GSEA, and WGCNA.
Currently, GO enrichment analysis supports 21 fruit species, while KEGG enrichment analysis supports 17.
GO enrichment
Users can upload a custom gene list and select a species-specific background gene set for enrichment analysis.
Analyses are completed within seconds, with results displayed directly on the website, including both tabular outputs and bubble plot visualizations. Downloadable result files are available for all analyses.
The platform will return various visualization charts to display enrichment analysis results.
KEGG enrichment
KEGG enrichment analysis can also be performed by uploading a gene list and selecting a species-specific background gene set.
GSEA
GSEA analysis against GO and KEGG gene sets is supported. Users can upload custom ranked gene lists and quickly obtain enrichment results, with multiple statistical charts available for visualization.
The platform will return various visualization charts to display GSEA results.
WGCNA
For the WGCNA online tool, users can upload custom gene expression matrices and trait data. Results, including tables and various visualization charts, will be sent to the user's email.
The platform will return various visualization charts to display WGCNA results.
Expression Module
The “Expression” module presents transcriptomic sequencing data related to fruit ripening for each fruit species. This includes sample processing information, differentially expressed genes (DEGs), and results from Gene Ontology (GO) enrichment analysis.
Download Module
The “Download” module provides datasets including ripening-related genes and transcriptomic analysis results.
