Gene Regulatory Networks (GRNs) allow the study of regulation of gene expression of whole Fly T-WEoN together with its step-by-step guide is available at. 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. Fly T-WEoN is available as a Cytoscape application that permits integration with other tools and facilitates downstream network analysis. Experimental data files can be generated with several standard procedures and used solely when and if available. melanogaster obtained from the literature. Fly T-WEoN is based on heuristic rules that reflect current knowledge on gene regulation in D. 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. Unlikely regulations are removed by applying a series of knowledge-based filters. 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. Even so, little is known at whole genome scale for most genes and contexts. The regulation of gene expression is a key factor in the development and maintenance of life in all organisms.

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