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CyExpDB: a web-based multi-species tissue-specific gene expression platform for functional genomics in Cyprinidae
Princy Saini1,2, Kunal Chaudhary1, Jutan Das1
1Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, Library Avenue, PUSA, New Delhi 110012, India.
Database : the Journal of Biological Databases and Curation
|December 31, 2025
Summary
A new database, CyExpDB, offers comprehensive transcriptomic data for key freshwater fish species. This resource aids researchers in aquaculture, evolutionary biology, and breeding by enabling detailed gene expression analysis.
Area of Science:
- * Genomics and Bioinformatics
- * Aquaculture and Fisheries Science
Background:
- * Freshwater fish, particularly Cyprinidae, are crucial for global food security and economic development.
- * Limited comprehensive transcriptomic data hinders functional genomics and breeding advancements in major Cyprinidae species.
Purpose of the Study:
- * To create a centralized, accessible database of transcriptomic data for key freshwater Cyprinidae species.
- * To facilitate functional genomics research, molecular breeding, and evolutionary studies in fish.
Main Methods:
- * Systematic analysis of 1582 RNA-seq samples from 190 BioProjects.
- * Integration of data covering 107 tissues and cell types across five species: Cyprinus carpio, Carassius gibelio, Carassius auratus, Labeo rohita, and Ctenopharyngodon idella.
- * Development of CyExpDB, a relational gene expression database with advanced visualization and analysis tools.
Main Results:
- * Establishment of CyExpDB (https://cyexpdb.abrl.in/), a scalable relational database.
- * User-friendly interface for retrieving, filtering, and visualizing coding/non-coding gene expression.
- * Tools for identifying tissue-specific genes (tau score), functional annotations (GO, KEGG), and pathway enrichment.
Conclusions:
- * CyExpDB provides an invaluable resource for researchers in aquaculture, evolutionary biology, and molecular breeding.
- * The database accelerates discoveries in fish biology, aids in trait improvement, and supports conservation efforts.
- * Facilitates in-depth transcriptomic exploration for advancing freshwater fish research.
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