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Computational Molecular Biology 2014, Vol. 4, No. 10, 1-17
http://cmb.biopublisher.ca
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Figure 4 ChIP-seq tag distribution and identified peak information for gene
PEX14
are displayed. Red frame indicates the [-1k, 2k]
around TSS. The peak-end track indicates the peaks detected by Cisgenome
. The co-localized peak is localized in
intronic region just upstream of a repeat region. The peak in intron is supposed to have regulatory function
2.4 Base composition for co-localized peaks in gene
context
Because co-localized peaks differed from single-localized
peaks as was analyzed in previous sections, we were
curious to investigate the genomic features
underlying co-localized peaks. Adenine and
thymine nucleotides were more overrepresented in
co-localized peaks compared with single-localized
peaks (Table 4). Accordingly, guanine and cytosine
nucleotides were underrepresented in co-localized
peaks. Normally, CpG dinucleotides were rare in
vertebrate DNA because the cytosine in such
context tended to be methylated then turned into
by spontaneous deamination. TpG or CpA
would accumulate as deamination products of
methylated CpGs, as what was observed in a human
α-globin pseudogene
. In Table 4,
the TpG content was negatively proportional to the
CpG o/e ratio, but the TpG o/e ratio did not have
stringently negative tendency against CpG o/e ratio.
With respect to TpG o/e ratio, one exception was
me2me3 group, which was found to have larger
TpG content yet smaller TpG o/e ratio than control.
When extending from gene-context to genomic
scale, similar results were obtained in
Supplementary Table 5. Taken together, co-localization
and single-localization peaks had distinct
underlying genomic composition.
Table 5 CGI coverage rate for different types of localized peaks
Number (Coverage rate)
TSS-proximal peaks [-1k,2k]
Non-TSS-proximal peaks
All peaks
me1
5948 (0.12±0.3)
33086 (0.03±0.16)
39034(0.04±0.12)
me1me2
1278 (0.18±0.33)
1494 (0.05±0.20)
2772 (0.11±0.13)
me1me2me3
536 (0.34±0.37)
991 (0.06±0.22)
1527 (0.16±0.17)
me1me3
726 (0.35±0.43)
1907 (0.09±0.26)
2633 (0.16±0.12)
me2
3899 (0.35±0.43)
3124 (0.12±0.31)
7023 (0.24±0.20)
me2me3
1860 (0.42±0.33)
2960 (0.10±0.29)
4820 (0.23±0.51)
me3
13212 (0.75±0.41)
11262 (0.33±0.46)
24474 (0.56±0.48)