DNA Methylation Analysis Platform

This platform provides comprehensive tools for analyzing DNA methylation patterns to understand epigenetic regulation mechanisms. From quality control to differential methylation analysis and functional interpretation, our workflow helps you uncover epigenetic insights from your methylation sequencing experiments.

Decoding epigenetic regulation through methylation pattern analysis.

Data Input

Upload your DNA methylation data and associated metadata files.

Methylation Data

Supported formats: .bed, .bismark, .csv, .tsv

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Sample Metadata

Sample information with group assignments

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Genomic Regions (Optional)

Regions of interest (BED, GFF, GTF)

Select File

Expression Data (Optional)

Gene expression data for correlation analysis

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Required Data Format (BED)

Column	Description	Example
Chromosome	Chromosome name	chr1
Start	Start position (0-based)	10000
End	End position	10001
Methylation Level	Beta value (0-1)	0.85
Coverage	Number of reads	12

Quality Control Parameters

Set thresholds for filtering low-quality methylation data.

Sample Quality Filters

Minimum CpG Sites per Sample

Minimum Mean Coverage

Maximum Methylation Deviation

Z-score threshold for global methylation

Detection P-value Threshold

CpG Site Filters

Minimum Coverage per CpG

Minimum Samples with Data

Percentage of samples required to have data

Exclude Probes with SNPs

SNP Distance Threshold

Base pairs around probe to check for SNPs

Batch Effect Assessment

Batch Variable (from metadata)

PCA Components for Batch Check

Data Preprocessing

Normalization and preprocessing of methylation data.

Normalization Method

Select Normalization Approach

Batch Correction Method

Method

Number of Surrogate Variables

For SVA method only

Data Transformation

Value Transformation

Probe Masking

Smoothing Options (for WGBS/RRBS)

Smoothing Method

Window Size (bp)

Differential Methylation Analysis

Identify differentially methylated positions (DMPs) and regions (DMRs).

Comparison Settings

Group Variable (from metadata)

Reference Group

Test Method

Adjust for Covariates

Comma-separated from metadata

DMP Thresholds

Adjusted P-value Cutoff

Minimum Absolute Beta Change

Minimum M Value Change

Multiple Testing Correction

DMR Analysis Parameters

DMR Detection Method

Maximum Gap Between CpGs (bp)

Minimum Number of CpGs per DMR

Minimum Region Length (bp)

Regional Methylation Analysis

Analyze methylation patterns across different genomic regions.

Genomic Regions to Analyze

Predefined Regions

Hold Ctrl/Cmd to select multiple

Custom Regions (from uploaded file)

Promoter Region Analysis

Promoter Definition

Gene Annotation Source

Chromosomal Distribution

Chromosome Bin Size (kb)

Include Sex Chromosomes

Methylation-Expression Correlation

Analyze relationships between methylation levels and gene expression.

Correlation Parameters

Correlation Method

Genomic Window for Correlation

Base pairs around gene TSS

Minimum Correlation Coefficient

Correlation P-value Cutoff

Expression Data Parameters

Expression Data Type

Expression Normalization

Regression Models

Simple linear regression

Multiple regression (adjust for covariates)

Segmented regression (for non-linear relationships)

Functional Enrichment Analysis

Perform enrichment analysis on genes associated with differential methylation.

Enrichment Parameters

Gene Set Source

Gene Distance for DMPs (kb)

Maximum distance from gene for DMP association

Enrichment Database

Hold Ctrl/Cmd to select multiple

Species

Enrichment Analysis Parameters

Enrichment Test Method

Adjusted P-value Cutoff

Minimum Genes per Term

Maximum Genes per Term

Custom Gene Sets (Optional)

Upload Custom Gene Set File

GMT, CSV, or TSV format gene sets

Select File

Data Visualization

Select and view interactive visualizations of your methylation analysis results.

Methylation Distribution

Beta value distribution across samples

PCA of Methylation

Sample clustering by methylation profiles

DMP Volcano Plot

Differentially methylated positions

DMR Genome Browser

Visualize DMRs in genomic context

Chromosomal Distribution

Methylation patterns by chromosome

Regional Methylation

Profiles across gene regions

Methylation-Expression

Correlation scatter plots

Enrichment Results

Top enriched functional terms

Methylation Heatmap

Clustered DMP/DMR patterns

Analysis Results

View and download your DNA methylation analysis results.

No results available yet. Please upload data and run analysis first.

Total CpGs Analyzed

Differentially Methylated Positions

Differentially Methylated Regions

Associated Genes

Top Differentially Methylated Positions

Chromosome	Position	Gene	Region	Beta Change	Adjusted P-value

Top Differentially Methylated Regions

Chromosome	Start-End	Gene	CpGs	Mean Beta Change	Adjusted P-value