The regulation of gene expression is a key factor in the development and maintenance of life in all organisms. Even so, little is known at whole genome scale for most genes and contexts. We propose a method, Tool for Weighted Epigenomic Networks in Drosophila melanogaster (Fly T-WEoN), to generate context-specific gene regulatory networks starting from a reference network that contains all known gene regulations in the fly. Unlikely regulations are removed by applying a series of knowledge-based filters. Each of these filters is implemented as an independent module that considers a type of experimental evidence, including DNA methylation, chromatin accessibility, histone modifications and gene expression. Fly T-WEoN is based on heuristic rules that reflect current knowledge on gene regulation in D. melanogaster obtained from the literature. Experimental data files can be generated with several standard procedures and used solely when and if available. Fly T-WEoN is available as a Cytoscape application that permits integration with other tools and facilitates downstream network analysis. In this work, we first demonstrate the reliability of our method to then provide a relevant application case of our tool: early development of D. melanogaster. Fly T-WEoN together with its step-by-step guide is available at https://weon.readthedocs.io.

基因表达的调节是所有生物体生命发育和维持的关键因素。即便如此，对于大多数基因和背景，在全基因组规模上仍知之甚少。我们提出了一种方法，即黑腹果蝇加权表观基因组网络工具(Fly T-WEoN)，从包含所有已知基因调控的参考网络开始生成特定于上下文的基因调控网络。通过应用一系列基于知识的过滤器来删除不太可能的法规。这些过滤器中的每一个都作为一个独立的模块实现，该模块考虑了一种实验证据，包括 DNA 甲基化、染色质可及性、组蛋白修饰和基因表达。Fly T-WEoN 基于启发式规则，反映了当前关于基因调控的知识D. melanogaster从文献中获得。实验数据文件可以通过几个标准程序生成，并且仅在可用时使用。Fly T-WEoN 可作为 Cytoscape 应用程序使用，允许与其他工具集成并促进下游网络分析。在这项工作中，我们首先证明了我们方法的可靠性，然后提供了我们工具的相关应用案例：D. melanogaster的早期开发。Fly T-WEoN 及其分步指南可在 https://weon.readthedocs.io 获得。