RegNetwork 2025: an integrative data repository for gene regulatory networks in human and mouse

RegNetwork is an open-source gene regulatory network (GRN) database that comprehensively curates regulatory relationships among transcription factors (TFs), microRNAs (miRNAs), and genes in human and mouse. Establishing a systematic GRN database is pivotal for advancing researchers' understanding of gene interactions. Currently, regulatory interactions are scattered across diverse data resources, posing significant hurdles for their efficient utilization. Consequently, integrating various data types and accurately annotating them with confidence scores has become imperative. In this updated version, we have extensively revised regulatory relationships among TFs, miRNAs, and genes, introducing novel datasets involving long noncoding RNAs (lncRNAs) and circular RNAs (circRNAs). As of now, RegNetwork 2025 comprises 125 319 nodes, including 76 156 for human and 49 163 for mouse, along with 11 107 799 regulatory interactions, including 7 712 347 for human and 3 395 452 for mouse. Compared to its predecessor, RegNetwork 2025 has witnessed an over 95% increase in the total number of regulatory interactions. Furthermore, we have devised a scoring system to quantify the reliability of regulatory relationships, enabling us to assemble a more trustworthy core dataset for users. The incorporation of lncRNA and circRNA has enriched the regulatory interaction types in RegNetwork 2025 and enhanced the accessibility of diverse data types. Data are freely available at http://www.zpliulab.cn/RegNetwork/home.