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Table 3 Large blocks of aberrant methylation identified in normal versus hyperplastic, adenoma, or cancer samples

From: Large hypomethylated blocks as a universal defining epigenetic alteration in human solid tumors

  Blocks (n) Total Mb inside blocks Intersection with colon blocks (%) 25%length quartile (Mb) 50%length quartile (Mb) 75%length quartile (Mb) Median diff value Hypo-meth. (%)
Breast (Cancer-normal) 150 42.87 92 0.15 0.2 0.36 −0.097 83
Breast (DCIS-normal) 349 77.94 91 0.11 0.17 0.28 −0.078 79
Colon (Cancer-normal) 1889 746.93 100 0.16 0.28 0.53 −0.11 100
Colon (Adenoma-normal) 1917 576.63 79 0.13 0.22 0.38 −0.068 100
Lung (Cancer-normal) 702 217.72 87 0.14 0.23 0.38 −0.088 98
Pancreas (ACA-normal) 1114 183 53 0.087 0.14 0.2 −0.061 52
Pancreas (IPMN-normal) 1349 274.09 55 0.099 0.16 0.26 −0.09 99
Pancreas (NET-normal) 683 136.9 69 0.0955 0.16 0.25 −0.16 98
Thyroid (Cancer-normal) 351 63.25 82 0.091 0.15 0.235 −0.054 78
Thyroid (Adenoma-normal) 266 49.9 90 0.09275 0.15 0.24 −0.049 77
  1. The `Blocks (n) column reports the total number of regions classified as blocks by our algorithm. `Total Mb inside blocks' is the total number of megabases contained by these blocks. The `Intersection with colon blocks (%) represents a comparison of the hypomethylated blocks for the comparison represented by the row, to the hypomethylated blocks identified between colon normal and cancer samples; note that 100% of colon blocks are inside colon blocks. We tested if overlaps this extreme can be due to chance and found P values <0.001 (0 occurrences in 1,000 permutations). The next three columns are the 25th, 50th, and 75th percentiles of block region sizes. The `Median diff value2019; is the median of the average difference between cases and controls are all regions defined as blocks. The `Hypo-meth. (%) column shows the percent of blocks that are hypomethylated.