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/).

中文翻译：

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CoFly：果蝇果蝇的基因共表达数据库。

果蝇果蝇可以用作研究生物医学和害虫管理中各种问题的模型生物。大量的果蝇转录组已通过微阵列在各种细胞类型，组织，发育阶段，毒理学暴露和其他条件下进行了分析。到目前为止，仍然没有开发用于探索这些宝贵数据的数据库。收集了来自美国国家生物技术信息中心基因表达综合中心的4,367个样品的微阵列数据，并通过加权基因共表达网络分析算法进行了分析。鉴定了五十一个与细胞类型，组织，发育阶段和其他实验条件有关的基因共表达模块。高维基因表达减少到数十个与实验/性状相关的模块，代表了表型的特征。六个模块富含簇状基因的基因组区域。集线器基因也可以通过模块内连接性进行筛选。通过分析高阶模块网络，我们发现小区信令模块比其他模块连接更多。基于模块的基因功能识别可能有助于发现新的基因功能。开发了一个易于使用的数据库，该数据库为果蝇的基因功能研究提供了新的资源（http://bioinformatics.fafu.edu.cn/fly/）。