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This article is part of the supplement: The International Conference on Intelligent Biology and Medicine (ICIBM) – Genomics

Open Access Research

Investigating the relationship of DNA methylation with mutation rate and allele frequency in the human genome

Junfeng Xia1, Leng Han1 and Zhongming Zhao1234*

Author Affiliations

1 Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA

2 Department of Psychiatry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA

3 Department of Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA

4 Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN 37232, USA

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BMC Genomics 2012, 13(Suppl 8):S7  doi:10.1186/1471-2164-13-S8-S7

Published: 17 December 2012

Additional files

Additional file 1:

The mutation rates at CpG sites inH1 and IMR90 cell lines. Refer to Figure 1 legend for interpretation of abbreviation.

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Open Data

Additional file 2:

The mutation rates for all CpG sites, methylated CpG sites and unmethylated CpG sites in different DNA strands. Refer to Figure 1 legend for interpretation of abbreviation.

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Open Data

Additional file 3:

The mutation rates for methylated CpG sites that are covered by different levels of sequencing reads. Refer to Figure 1 legend for interpretation of abbreviation.

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Open Data

Additional file 4:

The correlation between mutation rate and gene density for methylated CpG sites at the chromosome level. Each chromosome is plotted as a dot with its gene density per megabase and SNP density on the X and Y axis, respectively. The correlation coefficient (r2) is shown on the plot.

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Open Data

Additional file 5:

The mutation rates for CHG and CHH sites with different methylation levels. The X-axis includes CHH and CHG sites with different methylation levels (mC: methylated site; H_mC: highly methylated site (> 80%); HI_mC: high-intermediately methylated site (60-80%); I_mC: intermediately methylated site (40-60%); LI_mC: low-intermediately methylated site (20-40%); L_mC: lowly methylated site (≤ 20%)). The Y-axis is the mutation rate that was calculated as the density of SNPs at CHH and CHG sites.

Format: DOCX Size: 12KB Download file

Open Data

Additional file 6:

Human-chimpanzee divergence for methylated CpG sites in the human genome and intergenic regions. Refer to Figure 1 legend for interpretation of abbreviation.

Format: DOCX Size: 12KB Download file

Open Data