Statistical Methods in Systems Biology - Analysis of Epigenetic Data
Li et al give a nice overview of what is known about how the various epigenetic modifications affect transcription
Goldberg et al give an enthusiastic and simplified account of epigenetics.
Lieb & Clark argue that the main effect of all histone modifications is to clear the histones out of the path of genes to be activated. A key claim is that epigenetic mechanisms hide most TF targets. Is this plausible?
The ENCODE paper and its Supplement
Widschwendter et al investigate the relationship between PRC2 sites in stem cells and recurrent aberrant DNA methylation sites in cancer.
Our recent paper (Figures)on ALL/AML epigenomics addresses some issues of correlation analysis. Read mostly the correlation section and the integrative analysis.