Comparative (Computational) Analysis of the DNA Methylation Status of Trinucleotide Repeat Expansion Diseases
Table 3
Comparison of MEME results with patterns found in this study.
(a) 10 best 5 bp motifs in variably methylated regions
Pattern
MEME detail positive or negative strand
Our software variably methylated
TGTTT
FXN+, FMR1+
FMR1+, FXN+
AAACT
FXN++−
FXN++−
TATTT
FXN++
FXN
TCCAA
FXN+DMPK−
FXN+DMPK+
TCGAA
DMPK+DMPK−
DMPK+DMPK−
CTGAG
FMR1 − −
DMPK+FMR1+FMR1− −
CTGAA
FMR1−DMPK+
DMPK+FMR1−
GAGAG
FXN−FMR1+
FMR1++FXN
TA[CG]AA
DMPK−DMPK+
DMPK−DMPK+FXN−
ACCCA
DMPK− −
DMPK − −
(b) 10 best 5 bp motifs in always methylated regions
Pattern
MEME detail positive or negative strand
Our software always methylated
AGGGG
FXN_AM_1++FMR1
FMR1FXN_AM_1++
CCAGC
FXN_AM_1−FMR1−
FMR1 FXN_AM_1−
CTGGC
FXN_AM_2+FMR1+
FMR1 FXN+
CCACC
FXN_AM_2−FMR1+
FMR1 FXN_AM_2−
CCTCA
FMR1
FMR1+
CCGCC
FXN_AM_1−FMR1+
FXN_AM_1−FMR1+
AGCAC
FXN_AM_2−FMR1−
FXN_AM_2−FMR1+++−
AGTTG
FMR1++
FMR1+++FMR1
TAGCA
FMR1−FMR+
FMR1
AGAAA
FXN_AM_2+FMR1
FXN_AM_2+FMR1++
(c) 10 best 5 bp motifs in never methylated region
Pattern
MEME detail positive or negative strand
Our software never methylated
TTTGC
DMPK++−
DMPK
TTCTT
DMPK++
DMPK+++
AGGCA
DMPK
DMPK+−
TT[AT]CT
DMPK
DMPK++++
CCATC
DMPK+−
DMPK+−
CAGGC
DMPK++
DMPK
CAGAC
DMPK−+
DMPK+−
TGACG
DMPK++
DMPK++
ACC[AT]A
DMPK−+
DMPK+−
CTGGG
DMPK++
DMPK++
Key: + Positive strand. − Negative strand. FXN_AM_1 and FXN_AM_2 are two separated regions with always methylated CpG sites. Bold: Motif that MEME does not report all occurrences.