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Table 1 Reproducibility of newly detected peaks

From: A regression analysis of gene expression in ES cells reveals two gene classes that are significantly different in epigenetic patterns

  Fold Change Overlap of Chen Eland (%) Correlation of Peak Intensity
Eland Bowtie MAQ Soap2 Eland Bowtie MAQ Soap2 Eland Bowtie MAQ Soap2  
c-Myc 1.01 3.26 2.25 3.41 95.12 78.23 77.53 79.78 1.00 0.97 0.98 0.98
E2f1 1.03 1.34 1.36 1.40 85.41 74.67 74.83 75.70 1.00 0.98 0.99 0.99
Esrrb 2.88 3.12 3.29 3.93 99.10 88.62 89.01 90.22 1.00 0.82 0.83 0.83
Klf4 2.30 3.56 3.54 3.83 97.00 91.66 90.90 92.48 1.00 0.94 0.95 0.95
Nanog 1.01 2.15 1.84 2.42 97.93 87.93 90.06 91.69 1.00 0.97 0.99 0.99
n-Myc 1.86 3.24 3.59 3.60 95.39 84.22 85.71 86.15 1.00 0.97 0.97 0.97
Oct4 2.39 6.21 6.72 6.78 96.89 84.26 84.53 87.58 1.00 0.97 0.98 0.98
Smad1 1.49 3.19 3.24 3.53 91.56 75.58 79.84 81.62 1.00 0.85 0.86 0.88
Sox2 1.82 4.23 4.59 4.65 98.37 90.34 90.57 92.93 1.00 0.96 0.98 0.98
Stat3 1.60 8.49 4.80 8.33 97.09 80.99 81.70 84.64 1.00 0.97 0.98 0.98
Tcfcp2l1 1.04 1.73 1.54 1.85 89.05 90.80 91.13 92.73 0.99 0.98 0.99 0.99
Zfx 2.62 3.81 3.94 4.06 94.89 87.67 87.61 88.42 1.00 0.96 0.97 0.97
  1. Fold change is the ratio of newly detected peak number over the original peak number. Overlaps of the original peaks to the newly detected peaks were investigated with 200-bp window. The overlapped peaks were used to calculate the correlation of peak intensity.