NF-kB promoter architecture

Supplementary Data for Yang J, Mitra A, Dojer N, Fu S, Rowicka M, Brasier A. "A probabilistic approach to learning chromatin architecture and accurate inference of the NF-kappaB/RelA regulatory network using ChIP-Seq", Nucleic Acids Research (2013)

The following material is available for downloading:

  1. High quality RelA ChIP-Seq peaks, a text file in BED format for visual inspection in UCSC Genome Browser
  2. Human genes likely to be regulated by RelA, ordered by their chances of being RelA regulated
  3. Human genes that have RelA peaks in their promoter region, sorted by their MACS significance scores
  4. Enriched GO terms for the three categories i.e. Biological Process, Cellular Component, Molecular Function in MS Excel format
  5. P-values of enrichment for overlap of our RelA ChIP-Seq peaks with ENCODEs TF ChIP-Seq peaks
  6. Pre-processed RelA ChIP-Seq sequencing data in FASTA format. The tar archive contains FASTA data compressed using 7zip, please click here to download 7z utility.
  7. Wiggle density graphs of the RelA ChIP-Seq peaks, for visualization of WIG format in UCSC Genome Browser. Each chromosome is displayed on its own track.

Our manuscripts related to this publication:

  1. Bing Tian, Jun Yang, and Allan R. Brasier, Two-Step Cross-linking for Analysis of Protein–Chromatin Interactions, Transcriptional Regulation: Methods and Protocols, Methods in Molecular Biology, vol. 809 (2012)
  2. David Nowak, Bing Tian, Allan R. Brasier, Two-step cross-linking method for identification of NF-κB gene network by chromatin immunoprecipitation, BioTechniques (2005)
    Contact: Abhishek Mitra, abmitra@utmb.edu

    Rowicka Lab Brasier Lab UTMB