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Fig. 1 | Journal of Hematology & Oncology

Fig. 1

From: Genome-wide profiling of 5-hydroxymethylcytosines in circulating cell-free DNA reveals population-specific pathways in the development of multiple myeloma

Fig. 1

Genome-wide profiling of 5hmC from cfDNA derived from EA and AA patients with MM and its precursors. Genome-wide 5hmC was profiled in patient-derived plasma cfDNA samples using the 5hmC-Seal and the next-generation sequencing. The 5hmC-Seal data summarized for gene bodies were the primary targets for differential analysis between MM and its precursors (MGUS + SMM, i.e., MGUS and SMM combined) in all samples, using multivariable logistic regression models, controlling for age, sex, and self-reported race/population. In addition, we performed differential analysis between EA and AA patients with MM only. A The captured 5hmC-Seal reads in cfDNA are more abundant in gene bodies relative to the flanking regions and depleted at the promoter regions, based on the GENCODE annotations (hg19). TSS: transcription start site; TES: transcription end site. B The captured 5hmC-Seal reads are enriched in histone modifications marking enhancers (H3K4me1 and H3K27ac) derived from B-cells and T-cells compared with other tissue types. The annotations for H3K4me1 and H3K27ac were obtained from the Roadmap Epigenomics Project. The standard error is shown as the error bar. C The heat map shows the top 63 differential gene bodies between MM and its precursors in the combined EA and AA patients. D Shown are the enriched KEGG pathways among the top 500 differential gene bodies between MM and its precursors in the combined EA and AA samples. The X-axis represents the ratio between the number of differential genes and the total genes in a given pathway. E The Co-expression Network Enrichment Analysis was performed for differential gene bodies between EA and AA to provide further biological insights. Specifically, three modules (Module 1: 254 genes; Module 2: 156 genes; and Module 3: 75 genes) are shown from the modular gene co-expression analysis using the top 500 differential gene bodies between AA and EA patients with MM as the input. NES: normalized enrichment score. F–H Shown are the protein–protein interaction networks constructed for the co-expression and/or interaction modules identified from differential gene bodies between EA and AA patients with MM

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