Topology and Evolution of Global Transcriptional Regulatory Networks Across the Klebsiella pneumoniae Pan-Genome

For the primary data analysis presented in this study, peak calling was performed with the parameters –“-nomodel --extsize 75”. Reproducible peaks present in both replicates were identified using BEDtools (v2.26.0). Peak annotation was performed using ChIPpeakAnno (v3.18.2). An alternative pipeline was implemented for independent validation (-f BAMPE), and the high-confidence peak sets generated have been fully deposited and made publicly available on Zenodo for community reuse and independent verification. Crucially, we emphasize that while the main text primarily evaluates and utilizes the "Signal value" metric to construct the core gene regulatory networks, this parallel dataset was an example explicitly provided to the community with the absolute biological fold enrichment relative to the negative control.