Multi-Species NF-κB / Transposable Element Analysis

Reproducible analysis code for a comparative genomics study of RELA (a core NF-κB subunit) binding across the human, mouse, and cow genomes, and its association with transposable elements (TEs).

The analysis quantifies how much of the NF-κB cis-regulatory repertoire is ancient and shared across mammals versus lineage-specific and TE-derived.

Contents

File	Description
NFKB_TE_study.Rmd	Detailed reproducible analysis — data processing, statistics, and figure generation
HTML report	Rendered output with generated figures

Reproducing the analysis

# R >= 4.x
rmarkdown::render("NFKB_TE_study.Rmd")

Data availability

• Sequencing data — ArrayExpress accessions E-MTAB-12212 and E-MTAB-12213
• Archived code and intermediate files — Zenodo 10.5281/zenodo.8156730

Citation

If you use this code, please cite:

Wang L, et al. Multi-species analysis of inflammatory response elements reveals ancient and lineage-specific contributions of transposable elements to NF-κB binding. Genome Research, 2025 doi:10.1101/gr.280357.124

@article{wang2025nfkb,
  title   = {Multi-species analysis of inflammatory response elements reveals ancient
             and lineage-specific contributions of transposable elements to NF-{\kappa}B binding},
  author  = {Wang, Liangxi and others},
  journal = {Genome Research},
  year    = {2025},
  doi     = {10.1101/gr.280357.124}
}

Contact

Liangxi Wang — lxwang1993@gmail.com