2.4. Enrichment Test of Functional Categories

In the public data of the REMC database at http://compbio.mit.edu/roadmap/, we downloaded the epigenetic annotation files of 25 chromatin states of 23 blood cells in 127 epigenomics studies [12,13]. The 14 main functional categories were obtained by merging 25 chromatin states with functionally related annotation categories into a single functional category. These annotation files were used to locate the 14 main functional regions of each methylation probe. After functional location of the DNAm probe, we quantified the ratio of transcript-associated DNAm significant probes to all probes in 14 major functional categories. Finally, the chi-square test was used to test the significance and positive or negative effects of enrichment with these significant methylation probes in each domain.