Epigenetic Databases and Computational Methodologies in the Analysis of Epigenetic Datasets Mate ´ Ongenaert OncoMethylome Sciences, Liege, Belgium I. Introduction II. Basic Epigenetic Tools A. CpG detection B. Transcription start site and translation start site C. Genome browsers, annotation databases, and mapping tools D. Bisulfite conversion E. Experimental design and analysis III. Epigenetic Databases A. Chromatin B. DNA methylation C. DNA methylation and cancer IV. Cancer Databases A. Oncomine B. The Roche Cancer Genome Database V. Computational Approaches in Epigenetics A. Promoter region analysis and epigenome prediction VI. Applications and Data Analysis in Cancer Epigenetics A. Reexpression analysis B. CpG array analysis C. ChIP-Chip/ChIP-Seq data analysis D. Showcase: Analysis of a DNA-methylation dataset in CRC VII. Conclusions Acknowledgments References Advances in Genetics, Vol. 71 0065-2660/10 $35.00 Copyright 2010, Elsevier Inc. All rights reserved. DOI: 10.1016/S0065-2660(10)71010-5 9