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:
- High quality RelA ChIP-Seq peaks, a text file in BED format for
visual inspection in UCSC Genome Browser
- Human genes likely to be regulated by RelA, ordered by their chances of being RelA regulated
- Human genes that have RelA peaks in their promoter region, sorted by their MACS significance scores
- Enriched GO terms for the three categories i.e. Biological Process, Cellular Component, Molecular Function in MS Excel format
- P-values of enrichment for overlap of our RelA ChIP-Seq peaks with ENCODEs TF ChIP-Seq peaks
- 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.
- 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.
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Our manuscripts related to this publication:
- 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)
- 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 | |