整理了单个基因的DNA甲基化探针的部分可视化分析图。
甲基化差异
用来自5个受感染个体(F1-11, F1-12, S2, S3, S4)和100个健康个体的LRS数据，测定了全血DNA中GIPC1中扩展GGC重复区甲基化状态;甲基化在opdm患者和对照组之间没有显著差异。【@Deng.2020】
甲基化差异
CXCL12和IL7R基因区域的DNA甲基化位点。
这个使用的是在线工具：http://maplab.imppc.org/wanderer/
Ref：Diez-Villanueva A, Mallona I, Peinado MA. Wanderer, an interactive viewer to explore DNA methylation and gene expression data in human cancer. Epigenet Chromatin (2015) 8:22. doi: 10.1186/s13072-015-0014-8
甲基化差异
Figure 3. Differential DNA methylation uniquely associated to SLE or to pSS. (A) Box plots showing DNA methylation levels at unique DMCs in SLE compared to controls at FADD and HIF3A.
分析方法：minfi包。
文中还有提高EWASs的统计分析方法。
Ref: Shared and Unique Patterns of DNA Methylation in Systemic Lupus Erythematosus and Primary Sjögren's Syndrome . Frontiers in Immunology, 2019.
URL=https://www.frontiersin.org/article/10.3389/fimmu.2019.01686
DOI=10.3389/fimmu.2019.01686
甲基化差异
Fig. 3 Detailed DNA methylation map of the CHRNE gene. a (i) Boxplot and dot-plot of DNA methylation for individual neonatal control and ART samples at the two probes within the CHRNE gene that showed a significant difference between groups (adjusted p-value <0.05 (Bayesian levene’s test)). n =207 biologically independent birth samples, n =233 biologically independent adult samples. (ii) Boxplot and dot-plot of the same two probes in individual adult control and ART samples. The change is no longer significant in adult samples after correction for multiple testing, but the direction of methylation change persists. Boxplot elements are: center line-median; box limits-upper (Q3) and lower (Q1) quartiles; whiskers–smallest and largest non-outlier; points-outliers. b. Map of the CHRNE gene in hg19, showing EPIC probe locations. c Mean DNA methylation level at CHRNE for neonatal and adult non-ART and ART groups. Error bars are 95% confidence intervals. DMR1 is split into two: DMR1a that shows both ART and age specific DNA methylation differences and DMR1b that only shows ART-specific DNA methylation change. In addition, an age-specific DMR (DMR2) and a DMP are highlighted
方法：MissMethyl and minfi packages；文章里面还有讲到DMR和DMP的分析。
Ref：NOVAKOVIC B, LEWIS S, HALLIDAY J, et al. Assisted reproductive technologies are associated with limited epigenetic variation at birth that largely resolves by adulthood[J]. Nature communications, 2019, 10(1):3922. DOI: 10.1038/s41467-019-11929-9.
甲基化和基因表达的相关性
Matched methylation and gene expression data from The Cancer Genome Atlas were plotted to illustrate the correlation for selected cancer testis antigens (CTAs): (A) MAGEA1, (B) PAGE2, (C) CT83, and (D) SMC1B. The x axes give the β value of the region of the CTA 200 bp upstream of the transcription start site (TSS200) as a degree of methylation. The y axes give the gene expression as log2 transformed 1+ reads per kilobase of transcript per million mapped reads values of RNAseq.
这里用到的是TSS200，而不是单个probe。
Ref: [1] DJUREINOVIC D, HALLSTRöM B M, HORIE M, et al. Profiling cancer testis antigens in non-small-cell lung cancer[J]. JCI Insight, 2016, 1(10):e86837. DOI: 10.1172/jci.insight.86837.
甲基化和基因表达的相关性
Graphical representation of correlation of DNA methylation and gene expression of DMP-DEG pairs. Red and blue dots represent SSc and HD individuals, respectively.
基因表达用Z-score的数据，甲基化也用normalized的数据。
Ref：[1] LI T, ORTIZ-FERNáNDEZ L, ANDRéS-LEóN E, et al. Epigenomics and transcriptomics of systemic sclerosis CD4+ T cells reveal long-range dysregulation of key inflammatory pathways mediated by disease-associated susceptibility loci[J]. Genome medicine, 2020, 12(1):81. DOI: 10.1186/s13073-020-00779-6.
甲基化和基因表达的相关性
Figure 2. Negative correlation of USP44 gene expression and DNA methylation across 12 cancer types.
X-axis from 0 to 1 represents the beta value of the USP44 CpG sites in each cancer type. Y-axis from 0 to 8 represents the USP44 gene expression value (log2(RSEM+1)) across 12 cancer types.
这个来自Oncotarget的一篇文章，
Ref：Wang XX, Xiao FH, Li QG, Liu J, He YH, Kong QP. Large-scale DNA methylation expression analysis across 12 solid cancers reveals hypermethylation in the calcium-signaling pathway. Oncotarget. 2017 Feb 14;8(7):11868-11876. doi: 10.18632/oncotarget.14417