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. 2013 Apr 17;41(11):e117. doi: 10.1093/nar/gkt242

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© The Author(s) 2013. Published by Oxford University Press.

This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com

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Figure 3. — Estrogen receptor over-expression is correlated with decreased methylation. All the images in this figure represent ways that users can visualize regions of differential methylation (using estrogen receptor, ESR1, in the TCGA breast cancer dataset). (A) Box plot: the average beta value for a normal sample is higher than the primary sample, indicating that this CpG island (mapped to ESR1) shows decreased methylation in breast tumors. The box plot shows the median, minimum, maximum and quartiles for beta values for each group. This figure was produced using the ‘Average by Island’ workflow. (B) Scatter plot: methylation levels of ESR1 are negatively correlated with RNA-Seq expression levels. Individual samples are colored based on their sample grouping. This figure was produced using the ‘Average by Island’ workflow. (C) Visualization of.wig files in Integrative Genomics Viewer: normal, primary and delta-beta values (primary beta − normal beta) are exported from COHCAP as.wig files. A.bed file of UCSC CpG islands is also included in the visualization. Visualization of the ESR1 gene shows that a large number of CpG sites show a consistent decrease in methylation in tumor samples, and the peak is centered around the ESR1 translation start site. This figure was produced using the ‘Average by Site’ workflow.