Methylation & gene expression

1. Methylation inhibit gene expression

2. MAGEA2B
MAGEA2B 0.5
0.5 0.4
Gene expression (2nd )
0.4 0.3 y = -0.121x + 0.083
y = -0.335x + 0.272 R² = 0.021
0.3 0.2
Gene expression
R² = 0.070
0.2 0.1
0.1 0
0 -0.1 0 0.2 0.4 0.6 0.8
-0.1 0 0.2 0.4 0.6 0.8 1
-0.2
-0.2 -0.3
-0.3 Methylation
Methylation
4
3.5 MAGEB2
3 MAGED2
2.5 1.5
2
Gene expression
y = 0.882x - 0.136
y = -1.704x + 1.308 1
R² = 0.039
1.5 R² = 0.039
Gene expression
0.5
1
0.5 0
0 0 0.1 0.2 0.3 0.4
-0.5
-0.5 0 0.2 0.4 0.6 0.8 1
-1
-1
Methylation
-1.5
Methylation
Methylation inhibit the MAGEB2
expression, increase life span

3. MAGEA11 MAGEA11
2
2
1.5
1.5
Gene expression (2nd)
Gene Expression
1
y = 0.135x - 0.031 1
y = 0.628x - 0.167
0.5 R² = 0.001
0.5 R² = 0.021
0
0
0 0.2 0.4 0.6 0.8 1
-0.5 0 0.1 0.2 0.3 0.4 0.5 0.6
-0.5
-1
Methylation -1
Methylation
MAGEH1
1.2
MAGEH1
1 1.2
0.8 1
y = 0.736x - 0.102
0.8
Gene expression (2nd)
Gene expression
0.6 R² = 0.049
0.4 0.6
y = 0.331x - 0.086
0.2 0.4 R² = 0.022
0 0.2
-0.2 0 0.05 0.1 0.15 0.2 0.25 0.3 0.35 0
-0.4 -0.2 0 0.1 0.2 0.3 0.4 0.5 0.6 0.7
-0.6 -0.4
-0.8 -0.6
Methylation -0.8
Methylation

4. MAGED1 MAGED1
2.5
2.5
2
2
y = -0.309x + 0.2 1.5
1.5 R² = 0.000
1
Gene expression
Gene expression
1
0.5
0.5 y = -0.567x + 0.235
0
0 R² = 0.005
-0.5 0 0.1 0.2 0.3 0.4
-0.5 0 0.05 0.1 0.15 0.2 0.25
-1
-1
-1.5
-1.5
-2
-2 Methylation
Methylation
MAGEA12 MAGEA12
3
2.5 3
y = -0.276x + 0.239
2 R² = 0.001 2.5
Gene expression
1.5 2 y = -0.435x + 0.320
Gene expression
1 R² = 0.002
1.5
0.5 1
0 0.5
-0.5 0 0.2 0.4 0.6 0.8 1 0
-1 -0.5 0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8
Methylation Methylation
-1

5. MAGEC1
3.5
3
2.5
P=0,1274
Gene expression
2
y = -3.756x + 3.175
1.5 R² = 0.469
1
0.5
0
-0.5 0 0.2 0.4 0.6 0.8 1
-1
Methylation
MAGEC1
3.5
3
2.5
Gene expression
2
1.5
y = -2.115x + 1.684
1
R² = 0.193
0.5
0
-0.5 0 0.2 0.4 0.6 0.8 1 1.2
-1
Methylation

6. MAGEA8
4
3.5
3
2.5 y = -1.697x + 1.276
Gene expression
R² = 0.110
2
1.5
1
0.5
0
-0.5 0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1
-1
Methylation
MAGEA10 MAGEA10
5 5
4 4 y = -3.594x + 3.176
R² = 0.143
3 y = -4.002x + 3.595 3
Gene expression
Gene expression
R² = 0.138
2 2
1 1
0 0
0 0.2 0.4 0.6 0.8 1 1.2 0 0.2 0.4 0.6 0.8 1 1.2
-1 -1
-2 -2
Methylation Methylation

7. MAGEE1
0.4
y = 0.184x - 0.044
0.3
R² = 0.023
0.2
0.1
Axis Title
0
-0.1 0 0.1 0.2 0.3 0.4 0.5
-0.2
-0.3
-0.4
Axis Title
MAGEE1
0.4
y = 0.115x - 0.020
0.3 R² = 0.022
0.2
0.1
Axis Title
0
-0.1 0 0.1 0.2 0.3 0.4 0.5 0.6
-0.2
-0.3
-0.4
Axis Title

8. MAGEA5
0.4
0.3
0.2 y = -0.038x + 0.022
R² = 0.001
0.1
Axis Title
0
-0.1 0 0.2 0.4 0.6 0.8 1
-0.2
-0.3
-0.4
Axis Title
MAGEA5
0.4
y = -0.028x + 0.023
0.3 R² = 0.000
0.2
0.1
Axis Title
0
-0.1 0 0.2 0.4 0.6 0.8 1
-0.2
-0.3
-0.4
Axis Title

9. MAGEB3
0.4
0.3 y = 0.140x - 0.075
0.2 R² = 0.019
0.1
Axis Title
0
-0.1 0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8
-0.2
-0.3
-0.4
Axis Title
MAGEB3
0.4
0.3 y = 0.195x - 0.071
0.2 R² = 0.026
0.1
Axis Title
0
-0.1 0 0.1 0.2 0.3 0.4 0.5 0.6 0.7
-0.2
-0.3
-0.4
Axis Title

10. MAGEA6
y = -0.365x + 0.248
0.4 R² = 0.130
0.3
0.2
0.1
Axis Title
0
0 0.2 0.4 0.6 0.8 1
-0.1
-0.2
-0.3
-0.4
Axis Title
MAGEA6
0.4
0.3 y = -0.371x + 0.260
R² = 0.144
0.2
0.1
Axis Title
0
-0.1 0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1
-0.2
-0.3
-0.4
Axis Title

11. MAGEB4
0.7
0.6
0.5 y = 0.223x - 0.114
0.4 R² = 0.067
0.3
Axis Title
0.2
0.1
0
-0.1 0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8
-0.2
-0.3
-0.4
Axis Title
MAGEB4
0.7
0.6
0.5
0.4 y = 0.246x - 0.157
0.3 R² = 0.104
Axis Title
0.2
0.1
0
-0.1 0 0.2 0.4 0.6 0.8 1
-0.2
-0.3
-0.4
Axis Title

12. Axis Title
MAGEE2
0.5
0.4 y = -0.128x + 0.025
MAGEA9B
0.3 R² = 0.016 5
0.2 4
0.1
3 y = -3.405x + 2.928
0
R² = 0.037
Axis Title
-0.1 0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 2
-0.2 1
-0.3
0
-0.4
0 0.2 0.4 0.6 0.8 1
Axis Title -1
-2
Axis Title
MAGEB18
0.25
0.2 y = 0.027x - 0.034
0.15 R² = 0.001
0.1
0.05
Axis Title
0
-0.05 0 0.2 0.4 0.6 0.8 1
-0.1
-0.15
-0.2
-0.25
-0.3
Axis Title

13. MAGEC3 MAGEC3
0.4
0.4
0.3
0.3
0.2
0.2
0.1
0.1
Axis Title
y = -0.003x + 0.001
Axis Title
y = -0.000x + 0.000 0
0 R² = 2E-05
R² = 1E-06 -0.1 0 0.2 0.4 0.6 0.8 1
-0.1 0 0.2 0.4 0.6 0.8 1
-0.2
-0.2
-0.3
-0.3
-0.4
-0.4
-0.5
-0.5 Axis Title
Axis Title

14. 1.5
MAGED1 1 MAGED2
2.5
2 0.5
y = 0.882x - 0.136
Axis Title
1.5 R² = 0.039
0
1 0 0.05 0.1 0.15 0.2 0.25 0.3 0.35 0.4
Axis Title
0.5 -0.5
y = -0.309x + 0.2
0 R² = 0.000 -1
-0.5 0 0.05 0.1 0.15 0.2 0.25
-1 -1.5
Axis Title
-1.5
-2
Axis Title

15. MAGED4 (1)
3
2.5
2
1.5 MAGED4 (2)
1
Axis Title
3
0.5
2.5
0
2
-0.5 0 0.1 0.2 0.3 y = -1.886x + 0.367 0.5
0.4 0.6
R² = 0.066 1.5
-1
1
Axis Title
-1.5
0.5
-2
Axis Title 0
-0.5 0 0.1 0.2 0.3 0.4 y = -1.651x + 0.416
0.5 0.6 0.7
-1 R² = 0.121
-1.5
-2
Axis Title

16. P=0,0703
Km5

17. Km2

18. Km7

19. Km1

20. Km3

21. Km4
P=0,0734

22. Km6
P=0.0026

23. Correlation of methylation and gene
expression

25. (A) Correlation between ID4
expression and ID4 promoter
methylation in human breast
cancer
For this purpose, a part of the same breast cancer
cohort (n = 46) used previously for methylation
analysis was re-assessed (Figure 2A ).
We found an increased risk for tumour recurrence in
breast cancer patients with ID4 promoter methylation
(P = 0.036) compared to patients with lack of ID4
methylation (Figure 2B ).

26. Methylation headmap of MAGE genes?

27. MAGEE1
The sequence you input has 13375 nucleotides in length. There are 2 possible CpG island(s) found.
Homo sapiens melanoma antigen family E, 1 (MAGEE1), RefSeqGene on chromosome X.
CDS 5279..8152
MAGEE2
There are NO possible CpG islands found.
Homo sapiens melanoma antigen family E, 2 (MAGEE2), RefSeqGene on chromosome X.

28. MAGEC1
Homo sapiens melanoma antigen family C, 1 (MAGEC1), RefSeqGene on chromosome X.
Homo sapiens melanoma antigen family A, 2B (MAGEA2B), mRNA

29. Homo sapiens melanoma antigen family A, 11
(MAGEA11), RefSeqGene on chromosome X

30. Homo sapiens melanoma antigen family A, 10 (MAGEA10), transcript
variant 1, mRNA
NCBI Reference Sequence: NM_001011543.2
Homo sapiens melanoma antigen family B, 18 (MAGEB18), RefSeqGene on
chromosome X
NCBI Reference Sequence: NG_016370.1

31. Homo sapiens melanoma antigen family C, 3 Homo sapiens melanoma antigen family D, 1
(MAGEC3), RefSeqGene on chromosome X (MAGED1), RefSeqGene on chromosome X
NCBI Reference Sequence: NG_012559.1
NCBI Reference Sequence: NG_013272.1

32. Homo sapiens melanoma antigen
Homo sapiens melanoma antigen family
family H, 1 (MAGEH1), RefSeqGene
D, 2 (MAGED2), RefSeqGene on
on chromosome X chromosome X
NCBI Reference Sequence: NCBI Reference Sequence: NG_012844.1
NG_013248.1

33. Homo sapiens melanoma antigen family B, 4
(MAGEB4), RefSeqGene on chromosome X
NCBI Reference Sequence: NG_015870.1

34. Homo sapiens melanoma antigen family B, 1 (MAGEB1), RefSeqGene
on chromosome X
NCBI Reference Sequence: NG_016336.1

35. Homo sapiens melanoma antigen family A, 3 (MAGEA3), RefSeqGene on
chromosome X
NCBI Reference Sequence: NG_013244.1
There are 1 possible CpG island(s) found.
Homo sapiens melanoma antigen family A, 6 (MAGEA6), transcript variant 2, mRNA
NCBI Reference Sequence: NM_175868.1

36. Homo sapiens melanoma antigen family A, 5 (MAGEA5), RefSeqGene
on chromosome X
NCBI Reference Sequence: NG_016417.1

37. Homo sapiens MAGED4 protein (MAGED4) mRNA, complete cds
GenBank: AF329733.1
There are 2 possible CpG island(s) found.
http://www.urogene.org/methprimer

38. Homo sapiens melanoma antigen family B, 10 (MAGEB10), RefSeqGene on
chromosome X
NCBI Reference Sequence: NG_017094.1
There are 1 possible CpG island(s) found.

39. Homo sapiens melanoma antigen family C, 2 (MAGEC2), RefSeqGene
on chromosome X
NCBI Reference Sequence: NG_015872.1

40. Homo sapiens melanoma antigen family B, 2 (MAGEB2), RefSeqGene
on chromosome X
NCBI Reference Sequence: NG_013246.1
PREDICTED: Homo sapiens melanoma antigen family B, 5 (MAGEB5), mRNA
NCBI Reference Sequence: XM_293407.7

41. Homo sapiens melanoma antigen family A, 12
(MAGEA12), RefSeqGene on chromosome X
NCBI Reference Sequence: NG_015852.1
Homo sapiens melanoma antigen family A, 9 (MAGEA9), mRNA
NCBI Reference Sequence: NM_005365.4