Introduction

This report presents identified differential methylation cytosines (DMCs) and regions (DMRs).

Workflow of data processing

A brief summary of the data workflow:

  1. Data filtering: cytosines with \(read~depth \ge 5\) in \(\ge 2 ~samples\) in a group are kept, otherwise removed for that group before downstream analyses.

  2. Detecting DMCs and DMRs: DMCs are detected with dss and DMRs are detected with dss. Significant DMCs and DMRs have \(FDR \le 0.05\) (if P values are provided by statistical method) and \(absolute~methylation~difference \ge 0.1\).

  3. Annotation of DMRs: the genes overlapped with any DMR are identified. Here an overlapped gene is defined as at least 1% of the gene region is covered by any DMRs. The gene region is defined as the genomic region between transcription start and end, plus the upstream 1000 basepairs.

  4. Functional enrichment analyses of the overlapped genes: the overlapped genes identified in previous step are input into g:Profiler for functional enrichment analysis.

  5. Plots: some plots such as heatmaps are generated to visulize the results.

  6. Downloads: all result files are available for downloading at the Downloads section.

Sample information

Here is a table of samples used for DMC/DMR analyses. The column group is used to group samples.

group sampleId
FFPE_NAT_Lung FFPE_NAT_Lung_1
FFPE_NAT_Lung FFPE_NAT_Lung_2
FFPE_Tumor_Lung FFPE_Tumor_Lung_1
FFPE_Tumor_Lung FFPE_Tumor_Lung_2
NAT_Liver NAT_Liver_1
NAT_Liver NAT_Liver_2
Tumor_Liver Tumor_Liver_1
Tumor_Liver Tumor_Liver_2

Distribution of methylation values

Before detecting DMCs/DMRs, here is an overview of the methylation level distributions at the both sample and group levels.

Per sample

This figure displays the distribution of methylation values of all cytosines (or a sampled subset for the sake of performance) for each sample using violin plot.