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. 2014 Dec 12;15(Suppl 10):S4. doi: 10.1186/1471-2164-15-S10-S4

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Copyright © 2014 Vandenbon et al.; licensee BioMed Central Ltd.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

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Flowchart of the main steps in this study. Step 1 is the identification of genomic regions marked by one or more histone modifications or transcription initiation events. In step 2 genomic regions are clustered according to their features and enhancer regions are defined. In step 3, enhancers are further classified into 13 classes according to the pre-stimulation binding by six principal TFs. We perform various more detailed analyses on these 13 classes of enhancers in step 4, including analysis of gene expression of nearby genes, binding by additional TFs, and changes in binding by principal TFs after stimulation. Main input data are marked in grey.