{"doi":"10.1093/nar/gkae1009","title":"iModulonDB 2.0: dynamic tools to facilitate knowledge-mining and user-enabled analyses of curated transcriptomic datasets","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.","journal":"Nucleic Acids Research","year":2024,"id":421454,"datarank":0.6497546737364084,"base_score":3.4339872044851463,"endowment":3.4339872044851463,"self_citation_contribution":0.515098080672772,"citation_network_contribution":0.13465659306363645,"self_endowment_contribution":0.515098080672772,"citer_contribution":0.13465659306363645,"corpus_percentile":69.36644233000696,"corpus_rank":3961,"citation_count":30,"citer_count":21,"citers_with_citation_signal":11,"citers_with_endowment":11,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.946,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2024-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":252604,"name":"Jayanth Krishnan","orcid":null,"position":1,"is_corresponding":false},{"id":5727,"name":"Gaoyuan Li","orcid":"0009-0003-4392-0966","position":2,"is_corresponding":false},{"id":1214251,"name":"Xuwen A Lou","orcid":null,"position":3,"is_corresponding":false},{"id":812990,"name":"Kevin Rychel","orcid":"0000-0002-4769-2804","position":4,"is_corresponding":false},{"id":1213764,"name":"Yuan Yuan","orcid":"0000-0002-9509-9167","position":5,"is_corresponding":false},{"id":1214252,"name":"Heera Bajpe","orcid":null,"position":6,"is_corresponding":false},{"id":703762,"name":"Arjun Patel","orcid":"0000-0003-1959-0445","position":7,"is_corresponding":false},{"id":682123,"name":"Donghui Choe","orcid":"0000-0003-1107-7380","position":8,"is_corresponding":false},{"id":1213765,"name":"Jongoh Shin","orcid":"0000-0002-5094-1912","position":9,"is_corresponding":false},{"id":1213766,"name":"Jeffrey T. A. Burrows","orcid":"0000-0001-6595-8736","position":10,"is_corresponding":false},{"id":468009,"name":"Patrick V. Phaneuf","orcid":"0000-0002-4122-6589","position":11,"is_corresponding":false},{"id":576108,"name":"Daniel C. Zielinski","orcid":"0000-0001-6452-483X","position":12,"is_corresponding":false},{"id":5441,"name":"Bernhard Ø. Palsson","orcid":"0000-0003-2357-6785","position":13,"is_corresponding":false},{"id":988639,"name":"Edward Catoiu","orcid":"0000-0001-8680-7291","position":0,"is_corresponding":true}],"reference_count":28,"raw_metadata":null,"created_at":"2026-07-19T01:57:36.298171Z","pmid":"39494532","pmcid":"PMC11701608","fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}