Overview

This super-track combines related tracks of ChIP-chip data generated by the Wadelius lab at Uppsala University, Sweden. ChIP-chip, also known as genome-wide location analysis, is a technique for isolation and identification of DNA sequences bound by specific proteins in cells, including histones. Histone methylation and acetylation serves as a stable genomic imprint that regulates gene expression and other epigenetic phenomena. These histones are found in transcriptionally active domains called euchromatin.

These tracks contain ChIP-chip data for transcription factors (such as HNF-3b) and acetylated histone H3 and H4 in cell lines including HepG2 (liver carcinoma). Experiments were also performed after cell treatment with Na-butyrate.

Credits

These experiments were performed in the Claes Wadelius lab, Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University. The statistical analysis was done at the Linnaeus Centre for Bioinformatics at Uppsala University. Microarrays were produced at the Sanger Institute.

References

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Rada-Iglesias A, Wallerman O, Koch C, Ameur A, Enroth S, Clelland G, Wester K, Wilcox S, Dovey OM, Ellis PD et al. Binding sites for metabolic disease related transcription factors inferred at base pair resolution by chromatin immunoprecipitation and genomic microarrays. Hum Mol Genet. 2005 Nov 15;14(22):3435-47.

Smyth GK. Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol. 2004;3:Article3.

Yang YH, Dudoit S, Luu P, Lin DM, Peng V, Ngai J, Speed TP. Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Res. 2002 Feb 15;30(4):e15.