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Fig. 2 | Clinical Epigenetics

Fig. 2

From: TWIST1 DNA methylation is a cell marker of airway and parenchymal lung fibroblasts that are differentially methylated in asthma

Fig. 2

Gene expression and DNA methylation differs between airway and parenchymal fibroblasts. Airway fibroblasts were used as reference. a Plot of 53,617 gene expression probes used in the analysis. Red/Blue = Benjamini-Hochberg FDR < 0.05. The horizontal dotted line indicates the p value corresponding to Benjamini-Hochberg FDR < 0.05. Red = greater expression in parenchymal fibroblasts, blue = greater expression in airway fibroblasts. b Plot of 414,592 CpG probes used in the analysis. Red/Blue = Bonferroni adjusted p value < 0.05. Airway fibroblasts were used as reference. Red = greater methylation in parenchymal fibroblasts, blue = greater methylation in airway fibroblasts. The horizontal dotted line indicates the p-value corresponding to adjusted p value 0.05. c Distribution of DNA methylation (beta) difference between airway and parenchymal fibroblasts in significant probes (Bonferroni adjusted p value < 0.05). Red line = difference in beta of 0.2, which approximates a 20% change, green line = beta difference of 0.5. Bars in red indicate an absolute beta difference greater than 0.5 between airway and lung fibroblasts (differential methylation > 50%). d Gene feature type for all analysis probes, all significant probes, significant probes with a difference in methylation greater than 50%. e CpG density for all analysis probes, all significant probes, significant probes with a difference in methylation greater than 50%. f Gene feature type for all analysis probes, all significant probes, significant probes with a decrease in methylation of greater than 50% and significant probes with an increase in methylation of greater than 50%. g CpG density type for all analysis probes, all significant probes, significant probes with a decrease in methylation of greater than 50% and significant probes with an increase in methylation of greater than 50%. UTR, untranslated region; TSS, transcription start site; Island, > 200 bp with > 50% GC percentage; Shore, up to 2 kb from a CpG island; N_Shore, North shore upstream of CpG island; S_Shore downstream of CpG island; Shelf, 2–4 kb from a CpG island; OpenSea, regions of the genome without any enrichment of CpG content [12, 13]

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