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Table 2 Pearson correlation of DNA methylation results (beta-values) between WGBS and HM450K bead array for the H1-hESC cell line, measured for different categories

From: Reducing the risk of false discovery enabling identification of biologically significant genome-wide methylation status using the HumanMethylation450 array

  Infinium I Infinium II
Category Unique probes Median Pearson corr. P-value Unique probes Median Pearson corr. P-value
High quality 25,199 0.06 0.95 NA 83,565 0.10 0.92 NA
Multimap map 917 0.08 0.93 3.43e-09 2,602 0.11 0.91 3.72e-03
Repeats 1,645 0.13 0.85 6.1e-141 11,026\ 0.11 0.79 9.03e-11
Indels 901 0.07 0.94 6.49e-02 2,993 0.10 0.91 8.32e-02
Bis-okay 2,734 0.07 0.95 7.74e-02 11,804 0.10 0.92 8.32e-02
SNP-at-CpG-C 1,074 0.09 0.93 7.07e-18 8,099 0.10 0.83 6.59e-05
SNP-at-CpG-G 1032 0.09 0.91 2.38e-21 7,488 0.10 0.82 2.42e-04
SNP-1 14,155 0.07 0.95 6.33e-12 40,426 0.10 0.91 2.30e-01
SNP > =2 7,067 0.07 0.94 2.36e-27 13,822 0.10 0.90 2.27e-01
  1. Each probe count is the number of probes unique to each category and contains only probes which appear on the array and have a matching WGBS beta value. Category definitions: High-quality - contains probes which are not affected by any genomic factors; Repeats - describes probes which hybridize to repetitive regions; Bis-okay – are probes which hybridize regions containing any C- > T SNP or T- > C SNP and are ‘ okay in bisulfite space; SNP-at-CpG-C and SNP-at-CpG-G - are probes which have SNPs at the interrogated C and its neighbouring G position, respectively; Indels - are probes which hybridize regions containing INDELs; Multimap - are probes which hybridize to multiple genomic loci; SNP-1 - are probes which contain only a single SNP anywhere in the body; and SNP > =2 - are probes which contain at least 2 SNPs anywhere in the probe body.The p-values represent the difference in beta-value distribution calculated using the Wilcox-rank sum test [39] and multiple tested corrected using the Benjamini-Hochberg method [40]. The median of the absolute difference between WGBS and HM450K bead array of each set is also shown.