CoFly: A gene coexpression database for the fruit fly Drosophila melanogaster

The fruit fly Drosophila melanogaster can be used as a model organism for studying various problems in biomedicine and pest management. A large number of fruit fly transcriptomes have been profiled in various cell types, tissues, development stages, toxicological exposures, and other conditions by microarray. Until now, there are still no database developed for exploring those precious data. Microarray data for 4,367 samples from National Center for Biotechnology Information Gene Expression Omnibus was collected, and analyzed by weighted gene coexpression network analysis algorithm. Fifty one gene coexpression modules that are related to cell types, tissues, development stages, and other experimental conditions were identified. The high dimensional gene expression was reduced to tens of modules that were associated with experiments/traits, representing signatures for phenotypes. Six modules were enriched with genomic regions of clustered genes. Hub genes could also be screened by intramodule connectivity. By analyzing higher order module networks, we found that cell signaling modules are more connected than other modules. Module-based gene function identification may help to discover novel gene function. An easy-to-use database was developed, which provides a new source for gene function study in the fruit fly (http://bioinformatics.fafu.edu.cn/fly/).