User Manual

Identify CpG sites located within 1Mb of a gene's transcription start site (TSS) that significantly correlate with its expression.

Step 1: Search & Filter

Select a cancer type and optionally filter by Gene Symbol, CpG ID, or Cancer Type.

Step 2: View Results

The results table displays significant associations. Click "Plot" to visualize.

Step 3: Interactive Visualization

• X-Axis: DNA Methylation (Beta Value)
• Y-Axis: Gene Expression (log2 normalized)
• Correlation: Negative correlation implies methylation silences gene expression.

Explore how methylation at miRNA loci affects the expression of downstream target genes.

Step 1: Search & Filter

Select a cancer type and optionally filter by miRNA Name, Target Gene, or Cancer Type.

Step 2: View Results

The results table displays significant associations. Click "Plot" to visualize.

Step 3: Interactive Visualization

• X-Axis: DNA Methylation (Beta Value)
• Y-Axis: Target Gene Expression
• Correlation: Inverse correlation suggests miRNA-mediated repression is modulated by methylation.

Explore associations between DNA methylation and imputed drug sensitivity (IC50) scores.

Step 1: Search & Filter

Select a cancer type and optionally filter by Drug Name or Gene Symbol.

Step 2: View Results

The results table displays significant associations. Click "Plot" to visualize.

Step 3: Interactive Visualization

• X-Axis: DNA Methylation (Beta Value) and M-Value (Log-converted)
• Y-Axis: Drug IC50 Score (Predicted Sensitivity)

Link methylation changes to the activity of biological pathways inferred by the PARADIGM algorithm.

Step 1: Search & Filter

Select a cancer type and optionally filter by Pathway Name or Gene Symbol.

Step 2: View Results

The results table displays significant associations. Click "Plot" to visualize.

Step 3: Interactive Visualization

• X-Axis: DNA Methylation (Beta Value)
• Y-Axis: Pathway Activity Score
• Correlation: Correlation indicates regulatory link between the CpG site and pathway activation.

Investigate how methylation levels correlate with the abundance of immune cell populations in the tumor microenvironment.

Step 1: Search & Filter

Select a cancer type and optionally filter by Immune Cell Type or Gene Symbol.

Step 2: View Results

The results table displays significant associations. Click "Plot" to visualize.

Step 3: Interactive Visualization

• X-Axis: DNA Methylation (Beta Value)
• Y-Axis: Immune Infiltration Score
• Correlation: Positive correlation suggests methylation promotes immune cell infiltration.