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Table 1 Gene and DMR cluster overlap

From: Genomic Clustering of differential DNA methylated regions (epimutations) associated with the epigenetic transgenerational inheritance of disease and phenotypic variation

(A) Gene clusters from FT, MT, SC, GC, PGC data sets and DMR cluster data sets

 

Number of Sites

Total Clusters

Gene in Cluster

Data Type

   

 Female Tissue (FT)

1052

28

221

Differential Gene Expression

   

 Male Tissue (MT)

2763

41

727

Differential Gene Expression

   

 Sertoli Cell (SC)

430

24

101

Differential Gene Expression

   

 Granulosa Cell (GC)

479

22

111

Differential Gene Expression

   

 Primordial Germ Cell (PGC)

739

15

138

Differential Gene Expression

   

 DMR

776

21

194

Differential DNA Methylation

   

 Background (BKG)

20917

59

7132

Locations of All Genes

   

(B) Overlap of gene and DMR clusters between FT, MT, SC, GC, PGC, and DMR and background (BKG)

 

FT(28)

MT(41)

SC(24)

GC(22)

PGC(15)

DMR(21)

BKG(59)

 FT(28)

28

14

8

8

2

5

18

 MT(41)

14

41

13

14

6

11

31

 SC(24)

8

13

24

4

4

2

15

 GC(22)

8

14

4

22

5

4

17

 PGC(15)

2

6

4

5

15

2

14

 DMR(21)

5

11

2

4

2

21

15

 BKG(59)

18

31

15

17

14

15

59

(C) Clusters overlap among datasets after removal of background gene clusters

 

FT(12)

MT(11)

SC(9)

GC(5)

PGC(2)

DMR(7)

 

 FT(12)

12

1

0

0

0

0

 

 MT(11)

1

11

0

1

1

1

 

 SC(9)

0

0

9

0

0

0

 

 GC(5)

0

1

0

5

0

0

 

 PGC(2)

0

1

0

0

2

0

 

 DMR(7)

0

1

0

0

0

7

 
  1. (A) Gene clusters from FT, MT, SC, GC, PGC, BKG, as well as DMR clusters. The total number of clusters in each of these datasets, and total number of genes or DMR in these clusters. (B) The overlap in number of sites among these clusters. (C) The unique clustering for each dataset after removal of the gene cluster background