iModulonDB: a knowledgebase of microbial transcriptional regulation derived from machine learning

Abstract

Independent component analysis (ICA) of bacterial transcriptomes has emerged as a powerful tool for obtaining co-regulated, independently-modulated gene sets (iModulons), inferring their activities across a range of conditions, and enabling their association to known genetic regulators. By grouping and analyzing genes based on observations from big data alone, iModulons can provide a novel perspective into how the composition of the transcriptome adapts to environmental conditions. Here, we present iModulonDB (imodulondb.org), a knowledgebase of prokaryotic transcriptional regulation computed from high-quality transcriptomic datasets using ICA. Users select an organism from the home page and then search or browse the curated iModulons that make up its transcriptome. Each iModulon and gene has its own interactive dashboard, featuring plots and tables with clickable, hoverable, and downloadable features. This site enhances research by presenting scientists of all backgrounds with co-expressed gene sets and their activity levels, which lead to improved understanding of regulator-gene relationships, discovery of transcription factors, and the elucidation of unexpected relationships between conditions and genetic regulatory activity. The current release of iModulonDB covers three organisms (Escherichia coli, Staphylococcus aureus and Bacillus subtilis) with 204 iModulons, and can be expanded to cover many additional organisms.

A multi-scale transcriptional regulatory network knowledge base forEscherichia coli

“…We have also applied ICA to transcriptomics datasets for two additional microbes, Bacillus subtilis (16) and Staphylococcus aureus (17), to identify their respective iModulon structures. All microbial iModulons can be explored through the interactive dashboards available at iModulonDB (18).…”

Mining all publicly available expression data to compute dynamic microbial transcriptional regulatory networks

“…Since the iModulon decomposition for an organism is a knowledge-base that will be of interest to a broad audience of microbiologists, we created an interactive website (iModulonDB.org) for researchers to explore published iModulons 45 . iModulonDB lists all iModulons identified for a dataset, which link to interactive dashboards for each iModulon.…”

Machine learning uncovers a data-driven transcriptional regulatory network for the Crenarchaeal thermoacidophile Sulfolobus acidocaldarius

“…Beyond the static plots provided in this manuscript, all generated iModulon data and interactive graphical summaries are available for interrogation online at iModulonDB.org (Rychel et al, 2021).…”

“…We also present various groupings of poorly characterized genes which warrant further study, given their importance in regulation of gene expression. Static graphical summaries of all S. acidocaldarius iModulons, including enriched gene members and iModulon activities, are presented in the Supplementary Information, with interactive summaries available on iModulonDB.org (Rychel et al, 2021).…”