4 Peak Annotations

Based on the consensus peaks (see here)

Software used: ChIPseeker & deepTools

  • Below shows top 10 peaks (based on the p-values of each peak)
  • Annotated peaks are available to download from here

4.1 No. of peaks by group

Venn Diagram of peak overlaps (all samples)

Figure 4.1: Venn Diagram of peak overlaps (all samples)

Venn Diagram of peak overlaps (female only)

Figure 4.2: Venn Diagram of peak overlaps (female only)

Venn Diagram of peak overlaps (male only)

Figure 4.3: Venn Diagram of peak overlaps (male only)

4.2 No. of peaks by chromosome

Table 4.1: No. of peaks by chromosome
seqnames FD FV MD MV
1 5974 5970 4926 4729
2 4026 4018 3245 3102
3 3261 3291 2582 2516
4 1876 1923 1436 1313
5 2635 2717 2059 1933
6 3115 3182 2465 2214
7 2784 2824 2252 2106
8 2070 2100 1659 1544
9 2655 2734 2261 2224
10 2514 2519 2005 1892
11 3324 3403 2798 2818
12 2695 2744 2170 2049
13 940 958 748 657
14 1996 2002 1617 1600
15 1897 1842 1594 1450
16 2373 2336 2173 2086
17 3271 3186 2759 2783
18 908 881 719 632
19 3477 3345 2987 2821
20 1766 1709 1441 1432
21 520 519 405 386
22 1643 1616 1417 1432
X 989 933 831 664

4.3 No. of genes enrichred in peaks

4.3.1 Non-intergenic peaks only

Venn diagram showing the number of enriched genes

Figure 4.4: Venn diagram showing the number of enriched genes

4.3.2 Peaks in TSS (<2kb)

Venn diagram showing the number of enriched genes

Figure 4.5: Venn diagram showing the number of enriched genes

4.4 Genomic feature of peaks

Table 4.2: % of genomic features
Feature FD FV MD MV
Promoter (<=1kb) 44.86 45.21 49.31 51.13
Promoter (1-2kb) 6.44 6.41 5.82 6.02
5’ UTR 0.27 0.26 0.32 0.26
3’ UTR 1.91 1.94 2.22 1.98
1st Exon 1.36 1.25 1.37 1.19
Other Exon 2.43 2.35 2.63 2.43
1st Intron 10.99 11.14 9.85 9.45
Other Intron 14.41 14.05 12.34 11.71
Downstream (<=300) 0.73 0.72 0.79 0.74
Distal Intergenic 16.59 16.66 15.37 15.09
Table 4.3: No of peaks by genomic features
Feature FD FV MD MV
Promoter (<=1kb) 25439 25660 22952 22691
Promoter (1-2kb) 3653 3638 2708 2672
5’ UTR 155 149 149 117
3’ UTR 1085 1100 1032 879
1st Exon 774 712 636 530
Other Exon 1377 1335 1226 1079
1st Intron 6235 6321 4584 4195
Other Intron 8172 7975 5742 5196
Downstream (<=300) 413 407 366 327
Distal Intergenic 9406 9455 7154 6697
Genomic feautres of peaks

Figure 4.6: Genomic feautres of peaks

4.5 Distance to TSS

Distance to TSS

Figure 4.7: Distance to TSS

4.6 Peak frequency over TSS

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## >> preparing promoter regions...  2021-02-16 21:48:00 
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## >> plotting figure...             2021-02-16 21:48:11
Peak frequency over TSS (<2kb)

Figure 4.8: Peak frequency over TSS (<2kb) 

## >> preparing promoter regions...  2021-02-16 21:48:12 
## >> preparing tag matrix...        2021-02-16 21:48:12 
## >> plotting figure...             2021-02-16 21:48:54
## >> preparing promoter regions...  2021-02-16 21:48:54 
## >> preparing tag matrix...        2021-02-16 21:48:55 
## >> plotting figure...             2021-02-16 21:49:29
Peak frequency over TSS (<5kb)

Figure 4.9: Peak frequency over TSS (<5kb)

4.7 Peak heatmap over TSS

Peak heatmap

Figure 4.10: Peak heatmap