Modulons

Modulons are groups of genes whose expression changes in a coordinated way across different conditions, representing a regulatory module in the transcriptome. They are usually discovered by applying unsupervised learning to large transcriptome datasets, using methods such as independent component analysis or nonnegative matrix factorization to decompose the data into modules. Each module corresponds to a modulon, defined by genes with correlated regulation patterns.

Identification and interpretation: The activity of a modulon is inferred from the data and reflects the regulatory state under specific conditions. Genes within a modulon often share regulatory motifs or are co-regulated by the same transcription factors or environmental signals. A modulon can include several regulons and may capture indirect regulatory effects or combinatorial control.

Relationship to regulons: Regulons are sets of genes directly controlled by a single regulator. Modulons provide a higher-level view, aggregating co-regulated genes across regulators and conditions to depict broader transcriptional responses.

Validation and resources: Modulation is validated by enrichment of promoter motifs, transcription factor binding data, or perturbation experiments. Databases such as iModulonDB catalog modulons in bacteria like Escherichia coli and Bacillus subtilis, supporting comparative analyses and functional interpretation.