DNA Methylation-miRNA-mRNA Integration Analysis



DNA methylation is a biological process and an important epigenetic modification. DNA methylation is the introduction of methylation groups into DNA molecules, but methylation does not change the sequence of genes, but changes the activity of DNA fragments, thereby inhibiting the expression of certain genes. In mammals, DNA methylation is essential for normal development and is closely related to many biological phenomena, including genome imprinting, X chromosome inactivation, transposable factor recruitment, aging, and carcinogenesis. Cytosine methylation is ubiquitous in eukaryotes and prokaryotes, and the rate of methylation varies greatly between species.

By integrating DNA methylation data, miRNA data, and transcriptome data, the regulatory mechanisms between them can be studied more systematically, such as a systematic two-level joint study of the molecular mechanisms of miRNA regulating gene expression and DNA methylation regulating gene expression. Algorithms are used to predict miRNA target genes, and the miRNA expression profile, mRNA expression profile, and DNA methylation expression profile are combined to find key miRNAs and their corresponding target genes and the methylation levels of their corresponding promoter regions. Through the three regulatory relationships, a relationship network is constructed to explore the mechanism of miRNA and DNA methylation involved in various complex regulatory events from the perspective of systems biology. Therefore, the joint analysis of DNA methylation, miRNA, and mRNA is of great significance to the study of the occurrence and development of diseases.

The methylation status of the H19 gene.Figure1. The methylation status of the H19 gene. (Morenomoya J M, et al. 2014)

Application Fields

In the field of biomedicine, the DNA methylation-miRNA-mRNA integration analysis is mainly used in the occurrence and development of diseases and basic scientific research:

  • The molecular mechanism of miRNA regulating gene expression.
  • The molecular mechanism of DNA methylation regulating gene expression.
  • Research on the mechanism of disease.
  • Biomarker screening.

What We Offer

As one of the experienced bioinformatics data analysis providers, CD Genomics offers established, cost-efficient and rapid turnaround analysis services for DNA methylation-miRNA-mRNA integration analysis. The raw input DNA methylation, miRNA and mRNA data can be produced from different sample types, such as cells, tissues, body fluids, serum, plasma and whole blood. We can use various formats of data for analysis such as raw data files, or other intermediate data formats. We provide our clients with the following data analysis services:

  • Provide integrated analysis of DNA methylation-miRNA-mRNA.
  • According to the different research purposes of the research, we will customize the exclusive analysis plan for you.
  • Use cutting-edge statistical analysis methods to provide you with accurate co-expression data analysis.
  • A complete and practical report summarizing all results, in addition to displaying analysis methods and results, also includes interpretation of biological significance.
  • The fast analysis cycle accelerates the pace of your research.

Data Analysis Technical Route

Flow chart showing DNA methylation-miRNA-mRNA integration analysis. - CD Genomics.Fig 2. Flow chart showing DNA methylation-miRNA-mRNA integration analysis.

Analysis Content Includes:

Based on DNA methylation, miRNA and mRNA data, CD Genomics provides you with a one-stop data analysis service. In addition to the following regular analysis content, we can also provide customized analysis services according to your requirements.

  • DNA methylation, miRNA and mRNA raw data quality control.
  • Statistical analysis of methylation.
  • Functional enrichment analysis of methylation-related genes GO.
  • Enrichment analysis of the metabolic pathway of methylation-related gene KEGG.
  • Association analysis of differential methylation and differential miRNA.
  • Association analysis between differential methylation and differential genes.
  • Related GO function annotation and metabolic pathway enrichment analysis.

Data Ready

Before data analysis, the first thing is to get your data ready. The raw data or intermediate data can be obtained from the following channels:

Channels of DNA methylation, miRNA, and mRNA input data. - CD Genomics

In order to process data more efficiently, we prefer to receive data files in the raw format, but we can also accept pre-normalized files. In addition, if you have any questions about the data analysis cycle, analysis content and price, please click online inquiry.

What's More

For DNA methylation-miRNA-mRNA integration analysis, if you don't have the raw data, CD Genomics will provide sequencing services such as WGBS, RRBS, microarray, MeDIP-seq and MRE-seq for DNA methylation data. In addition, we are able to provide services for obtaining and mining data from public databases (such as Roadmap, BLUEPRINT, etc.). For more detailed information, please feel free to contact us.


  1. Morenomoya J M, et al. The transcriptomic and proteomic effects of ectopic overexpression of miR-30d in human endometrial epithelial cells[J]. Molecular Human Reproduction, 2014, 20(6):550.
  2. Robertson KD. DNA methylation and human disease. Nat Rev Genet. 2005 Aug;6(8):597-610. doi: 10.1038/nrg1655. PMID: 16136652.

* For research use only. Not for use in clinical diagnosis or treatment of humans or animals.

Online Inquiry

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