biostudies-literatureLin HFundamental Research Funds for the Central UniversitiesNational Natural Science Foundation of ChinaNational Key Research and Development Program of Chinagkae1323https://www.ebi.ac.uk/biostudies/studies/S-EPMC11736433biostudies-literatureUnknown53(2)Enhancer clusters, pivotal in mammalian development and diseases, can organize as enhancer networks to control cell identity and disease genes; however, the underlying mechanism remains largely unexplored. Here, we introduce eNet 2.0, a comprehensive tool for enhancer networks analysis during development and diseases based on single-cell chromatin accessibility data. eNet 2.0 extends our previous work eNet 1.0 by adding network topology, comparison and dynamics analyses to its network construction function. We reveal modularly organized enhancer networks, where inter-module interactions synergistically affect gene expression. Moreover, network alterations correlate with abnormal and dynamic gene expression in disease and development. eNet 2.0 is robust across diverse datasets. To facilitatNucleic acids researchModular organization of enhancer network provides transcriptional robustness in mammalian development.PMC11736433320706352023YFC250810032071030924741042072023006832370586Liu LHuang JHong JHong DChen FLu FYe XLi LSun NZhang YChen WLin HYe KfalseModular organization of enhancer network provides transcriptional robustness in mammalian development.Enhancer clusters, pivotal in mammalian development and diseases, can organize as enhancer networks to control cell identity and disease genes; however, the underlying mechanism remains largely unexplored. Here, we introduce eNet 2.0, a comprehensive tool for enhancer networks analysis during development and diseases based on single-cell chromatin accessibility data. eNet 2.0 extends our previous work eNet 1.0 by adding network topology, comparison and dynamics analyses to its network construction function. We reveal modularly organized enhancer networks, where inter-module interactions synergistically affect gene expression. Moreover, network alterations correlate with abnormal and dynamic gene expression in disease and development. eNet 2.0 is robust across diverse datasets. To facilitat2025-01-01T00:00:00Z2025 Jan2026-04-19T03:29:20.287Z2025-04-04T02:46:51.709ZS-EPMC117364333981751610.1093/nar/gkae1323