Cancer Genetics and Epigenetics 2015, Vol.3, No.11, 1-8
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Table 1 Number of CpG sites in the internal stability samples
Mutation genes
DNMT3A
IDH
IDH_3AD
control
Stability sites
351382
368877
332008
465332
Table 2 The number of DMS
Mutation
Number of DMS
Number of N_DMS
DNMT3A
IDH
IDH_3AD
91981
67074
69555
210982
235889
233408
Finally, doing T test statistical analysis for differentially
methylated profile by using MeV v4.9 software, the
results suggest that 98% of the genes are
significant( ), indicating that the methylation
level of disease samples and normal samples have a
significant difference. Figure 3 is a T test chart. The
row represents samples and the column represents T
test value. Figure 3 suggests that there are significant
differences between the disease samples and normal
samples ( ).
2.2 Relationship between DNA methylation and
expression of different genomic regions
In the screened 1,452 genes, 1,235 gene expression
values can be found in disease and normal samples. These
1,235 genes classified into the following two groups:(1)
In the gene body. (2) Upstream 2 kb of the transcription
start site.1,012 genes fall on the gene body and 201
genes fall on the upstream 2kb of transcription start
site. In order to analyze the relationship between DNA
methylation and expression, firstly, for the gene body,
we calculate the mean DNA methylation value and the
mean expression value among samples, then the
disease samples and normal samples are put together,
make two variables (DNA methylation and expression )
correlation analysis using SPSS 19.0.Test results are
shown in Table 3:
As can be seen from Table 3, p value of Pearson,
Kendall, Spearman correlation coefficient was less
than 0.01. It suggests that DNA methylation and
expression in the gene body have a weak positive
correlation at 0.01 (unilateral) level.
The 1,012 genes in the gene body are separated from
disease group and normal group and they are drawn
correlation analysis diagram with R(R is a free
software environment for statistical computing and
graphics). As shown in Figure 4:
As can be seen from Figure 4, in the gene body, DNA
methylation and gene expression of disease samples
have a weak positive correlation. But hypermethylation
of the normal samples tends to low expression.
In the promoter, we use genes of fall into the promoter
and screen differentially methylated genes and
differentially expression genes using R package. Then
we calculate the number of hypermethylated genes
with low expression and the number of hypermethylated
genes with high expression, drawing relationship
diagram between DNA methylation and expression in
the promoter, as shown in Figure 5:
As can be seen from Figure 5, in the promoter, the
number of hypermethylation genes with low
expression is significantly more than the number of
hypermethylation genes with high expression. It can
be inferred that, in the promoter region,
hypermethylation sites prefer low expression.
2.3 Enrichment analysis results
We use the DAVID software to do functional enrichment
analysis for screened 1,452 genes, enriched to the
function directory and GO biological process results
shown in Table 4 below:
We enriched to the KEGG pathway for differentially
methylated genes, the results are shown in Table 5:
It can be seen in Table 4 and Table 5, differentially
methylated genes are encoding the phosphoprotein and
calcium. It played the main function of chromosomal
rearrangements, cell adhesion, leukocyte activation and
also played synaptic transmission, the process involved
in nucleotide metabolism, transcriptional regulation of
gene expression. Moreover, these differentially
Table 3 Correlation analysis table
Correlation coefficient p value
Correlation
Pearson 0.108**
Kendall 0.253**
Spearman 0.365**
p<0.05
p<0.05
p<0.05
Positive
Positive
Positive
01.0
p
01.0
p
