PRECISE 2.0 - an expanded high-quality RNA-seq compendium for Escherichia coli K-12 reveals high-resolution transcriptional regulatory structure

Abstract

AbstractUncovering the structure of the transcriptional regulatory network (TRN) that modulates gene expression in prokaryotes remains an important challenge. Transcriptomics data is plentiful, necessitating the development of scalable methods for converting this data into useful knowledge about the TRN. Previously, we published the PRECISE dataset for Escherichia coli K-12 MG1655, containing 278 RNA-seq datasets created using a standardized protocol. Here, we present PRECISE 2.0, which is nearly three times the size of the original PRECISE dataset and also created using a standardized protocol. We analyze PRECISE 2.0 at multiple scales, demonstrating multiple analytical strategies for extracting knowledge from this dataset. Specifically, we: (1) highlight patterns in gene expression across the dataset; (2) utilize independent component analysis to extract 218 independently modulated groups of genes (iModulons) that describe the TRN at the systems level; (3) demonstrate the utility of iModulons over traditional differential expression analysis; and (4) uncover 6 new potential regulons. Thus, PRECISE 2.0 is a large-scale, high-quality transcriptomics dataset which may be analyzed at multiple scales to yield important biological insights.