ArticleNucleic acids research2025
iModulonDB 2.0: dynamic tools to facilitate knowledge-mining and user-enabled analyses of curated transcriptomic datasets.
Article in Nucleic acids research, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Transcriptional regulatory network differences between six industrialMetabolic engineering communications · 2026Article
- iModulonMiner 2.0: multi-modality modularization of prokaryotic bulk, single-cell, and community omics data.Nucleic acids research · 2026Article
- Review
- Article
- DDTRN: predicting bacterial transcriptional regulatory networks based on gene sequences using dual descriptor.Briefings in bioinformatics · 2026Article
- Contrasts and similarities in the transcriptomic response to antimicrobial coinage metals inMicrobiology spectrum · 2026Article
- Revealing transcriptomic responses inmSystems · 2026Article
- Aerobicity stimulon iniScience · 2026Article
- Approaches for accelerating microbial gene function discovery using artificial intelligence.Nature microbiology · 2026Review
- The transcriptional regulatory network of the Escherichia coli MG1655 reference strain.Nucleic acids research · 2026Article
- Article
- groovDB in 2026: a community-editable database of small molecule biosensors.Nucleic acids research · 2026Article
- Laboratory Evolution Reveals Transcriptional Mechanisms Underlying Thermal Adaptation of Escherichia coli.Genome biology and evolution · 2025Article
- Elucidating the role of lipid metabolism dysregulation in the transition from oral lichen planus to oral squamous cell carcinoma.Journal of translational medicine · 2025Article
- Integrated genomic and proteomic analysis of the mouse-adaptedCurrent research in microbial sciences · 2025Article
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Authors and funding
14 authors.
Funding
Abstract
iModulons-sets of co-expressed genes identified through independent component analysis (ICA) of high-quality transcriptomic datasets-provide an unbiased, modular view of an organism's transcriptional regulatory network. Established in 2020, iModulonDB (iModulonDB.org) serves as a centralized repository of curated iModulon sets, enabling users to explore iModulons and download the associated transcriptomic data. This update reflects a significant expansion of the database-19 new ICA decompositions (+633%) spanning 8 925 expression profiles (+1370%), 503 studies (+2290%) and 12 additional organisms (+400%)-and introduces new features to help scientists decipher the mechanisms governing prokaryotic transcriptional regulation. To facilitate comprehension of the underlying expression profiles, the updated user-interface displays essential information about each data-generating study (e.g. the experimental conditions and publication abstract). Dashboards now include condition-specific coloring and highlight data generated from genetically perturbed strains, enabling users to rapidly interpret disruptions in transcriptional regulation. New interactive graphs rapidly convey omics-derived indicators (e.g. the explained variance of ICA decompositions, genetic overlap between iModulons and regulons). Direct links to operon diagrams (BioCyc) and protein-protein interaction networks (STRING) provide users with seamless access to external resources for further assessment of iModulons. Lastly, a new suite of search-driven and species-wide analysis tools promotes user-engagement with iModulons, reinforcing iModulonDB's role as a dynamic, interactive knowledgebase of prokaryotic transcriptional regulation.
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Registered trials
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