Large-scale analysis of zebrafish (Danio rerio) transcriptomes identifies functional modules associated with phenotypes.

Abstract

Zebrafish (Danio rerio) is an excellent model for biomedicine research due to its genetic accessibility and optical transparency. A large number of microarray based transcriptomes of zebrafish have been profiled in various cell types, tissues, development stages, toxicological exposures and other conditions. However, there is still no easy-to-use web tool to explore those precious data. We downloaded 1434 microarray data from National Center for Biotechnology Information Gene Expression Omnibus (NCBI GEO), constructed weighted gene co-expression network, and identified 50 modules of co-expressed genes that correspond to different cell types, tissues, development stages, and other experimental conditions. These modules were associated with experiments/traits, and may serve signature modules for phenotypes. Hub genes were screened by intra-modular connectivity. Higher-order module networks analysis suggested that nucleus and cell cycle modules are densely connected. Module-based gene function identification may help to discover novel gene function. Our web tool provides a new resource for gene function study in zebrafish (http://bioinformatics.fafu.edu.cn/zebrafish/).