IModulonMiner and PyModulon: Software for unsupervised mining of gene expression compendia.

ABSTRACT: Public gene expression databases are a rapidly expanding resource of organism responses to diverse perturbations, presenting both an opportunity and a challenge for bioinformatics workflows to extract actionable knowledge of transcription regulatory network function. Here, we introduce a five-step computational pipeline, called iModulonMiner, to compile, process, curate, analyze, and characterize the totality of RNA-seq data for a given organism or cell type. This workflow is centered around the data-driven computation of co-regulated gene sets using Independent Component Analysis, called iModulons, which have been shown to have broad applications. As a demonstration, we applied this workflow to generate the iModulon structure of Bacillus subtilis using all high-quality, publicly-available

SUBMITTER: Sastry AV 

PROVIDER: S-EPMC11534266 | biostudies-literature | 2024 Oct

REPOSITORIES: biostudies-literature