What are DMGs?

DMG stands for differentially methylated genes. A DMC is a gene that has at least one DMC on its gene body, promoter or flanking region.

Treatment and control groups

We used three groups - L1, L2 and L3 diets - to define DMGs. L1 diet was used as control.

Data sets for differential expression analysis

  • L2:L1: L2 vs. L1 with using L1 as control
  • L3:L1: L3 vs. L1 with using L1 as control

See Experimental feed for details about L1, L2 and L3 groups.

Definition of DMGs

We used methylKit to define DMCs with the following criteria.

  1. abs(percentage methylation differences) >= 20%
  2. Q-value < 0.01

We then defined DMGs as genes with at least one DMC in the following genomic regions.

Genomic regions for RRBS read mapping

  1. Exon
  2. Intron
  3. P250 (proximal promoter)
  4. P1K (promoter)
  5. P6K (distal promoter)
  6. Flanks (potential enhancer region)
Genomic regions for RRBS read alignment
Definition of genomic regions for RRBS read alignment.

Differentially methylated genes

There are no noticeable differences between L2:L1 and L3:L1 in terms of the number of DMGs.

Identified DMGs for L2:L1 and L3:L1

  • L2 vs. L1: 1998 DMGs
  • L3 vs. L1: 1997 DMGs

Most DMGs have only one DMC for both L2:L1 and L3:L1.

Analysis of DMGs

We further analysed DMGs to understand the differences of DNA methylation profiles affected by micronutrients.

Functional annotation databases

  • KEGG (Kyoto Encyclopedia of Genes and Genomes)
  • GO (Gene Ontology)

Functional annotation method

  • ORA (over representation analysis)

List of DMGs with gene symbols and gene names

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