CyExpDB: a web-based multi-species tissue-specific gene expression platform for functional genomics in Cyprinidae fish

This is the authors' abstract. We don't add key points for this paper.

Freshwater fish play a vital role in global food security and sustainable development, with the Cyprinidae family standing out due to its remarkable diversity and economic importance. Despite the increasing availability of high-quality genomic resources, comprehensive transcriptomic data for major Cyprinidae species remain limited, hindering progress in functional genomics and breeding. To address this, we systematically analysed 1582 RNA-seq samples from 190 BioProjects, covering 107 tissues and cell types across five key species: Cyprinus carpio, Carassius gibelio, Carassius auratus, Labeo rohita, and Ctenopharyngodon idella. This large-scale integration of transcriptomic data led to the development of CyExpDB (https://cyexpdb.abrl.in/), a relational gene expression database built on a robust scalable relational database architecture. CyExpDB offers a user-friendly interface for retrieving, filtering, and visualizing both coding and non-coding gene expression profiles, with advanced features for exploring tissue-specific genes, functional annotations, and pathway enrichment. Users can identify tissue-specific genes using the tau score, examine their biological roles through Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses, and compare expression patterns across tissues and species. CyExpDB offers an accessible resource for researchers in aquaculture, evolutionary biology, and molecular breeding. By enabling in-depth transcriptomic exploration, CyExpDB will accelerate discoveries in fish biology, support trait improvement, and inform conservation efforts.