*4.6. Methylation Modification of Gene Expression*

After the completion of independent methylome and transcriptome analyses, the correlation between methylation level and gene expression was progressively analyzed on four different levels. First, gene methylation level and gene expression densities were mapped onto the chromosomes of *P. mume*, and relationships between methylation levels and the expressions of promoters or gene coding regions, upstream (2-kb) and downstream (2-kb) regions, TSSs, and TESs were explored from a global perspective [48,90,108]. Second, CG, CHG, and CHH methylation modification patterns of DEGs (including promoters and 2-kb upstream and downstream regions) identified from the transcriptome data were analyzed [109,110]. Third, we attempted to relate the expression of DMR-related genes to different methylation modification patterns [111,112]. Finally, we identified the set of DMR-related genes that overlapped with DEGs, and subjected them to GO and KEGG enrichment analyses.
