1. CTCF Peaks

2. All CTCF Peaks 15 datasets
Cells: CH12, ER4, G1E, HPC7, LSK, NEU, TCD4, TCD8, ERY, MON
123,387 merged peaks
HPC7 has a more stringent cutoff, .01 for peaks

3. Peak length

4. Separating peaks by number of datasets

5. Intersect peak categories with ccREs
Split Peaks into low(1-4), mid(5-12) and high (13-15) and find overlaps with ccREs
26,550 / 83,816 = .32
18,384 / 26,416 = .70
12,833 / 13,154 = .98
Intersect peak categories with ccREs

6. Dominant IDEAS states for called peaks
Peak found in:
Low (1-4 datasets)
139,177 states
Medium (5-12 datasets)
209,074 states
High (13-15 datasets)
187,955 states
Dominant IDEAS states for called peaks
Sorted by state count in High grouping
One state per dataset with peak called per peak
7 C
13 CN
24 PENCA
25 T C
26 CNE T
States with CTCF signal

7. All States within peak set, except 0’s only counted when only state
Peak found in:
Low (1-4 datasets)
1,216,173 states
Medium (5-12 datasets)
566,212 states
High (13-15 datasets)
405,088 states
CTCF states are often in peaks, but not always the dominant state in the peak. Especially state 24 PENCA.
This also uses states from regions where they are not peaks in the cell type.
All states in all peaks (except 0’s when other states present)

8. Low category peaks in MultiView track

9. High category peaks in MultiView track

10. TAD boundaries Number of peaks overlapping end base of TADs
Low 185/83,816 = .002
Mid 141/26,416 = .005
High 139/13,154 = .011
Number of peaks overlapping end 20kb of TADs
Low 6,128/83,816 = .07
Mid 2,603/26,416 = .10
High 1,719/13,154 = .13
TAD boundaries
Boundaries computed as start + 1 and end – 1 and start – 20,000 to start, end – 20,000 to end.

11. Motifs from SeqUnwinder

12. Motifs from SeqUnwinder

13. Motifs from SeqUnwinder
On going run adding in ccREs

14. Other checks ORegAnno Regulatory regions 17,188
Intersect high peaks 509 CTCF peaks
Intersect low peaks 1,882 CTCF peaks
ORegAnno Transcription Factor binding sites 397,782
Intersect high peaks 5,926 CTCF peaks
Intersect low peaks 20,846 CTCF peaks
RefSeq Functional elements 1,968
Intersect high peaks 71 RefSeq Ele
Intersect low peaks 294 RefSeq Ele
Other checks
Oreganno sites are tested

15. Cell specific peaks HPC7 (13,141 peaks)
Used all peaks as background.
This has only 1 replicate and was only found in this dataset. One of largest peak numbers.
Number of cell specific peaks mostly reflects total number of peaks called. (G1E has only 1!)

16. Cell Specific peaks ERY (1,406 replicated peaks)
I required these to be in both replicates.

17. Cell specific peaks MON (1,307 peaks)

18. CTCF Peaks found in all 15 datasets (7,116 peaks)
I raised the cutoff for the FDR for these to .1 from Without this there were no terms.

19. Peak length by category
Average length
Median
Low
580
493
Mid
975
819
High
1364
1192
High unmerged
735
689

20. Worst case: 63 peaks merged to one
9 with 40 or more. 84 with 30 or more.
These would have been mid category without the single large peak merging them.

21. Same region with IDEAS
Should I use a window slid over the merged peaks, rather than the peaks themselves? If so what size? Homer peaks – 150, IDEAS windows – 200, ?

22. THE END

23. Second largest peak in high category

24. Slides from before filtering HPC7 peaks and looking for non-zero states

25. All CTCF Peaks 15 datasets 141,678 merged peaks
Cells: CH12, ER4, G1E, HPC7, LSK, NEU, TCD4, TCD8, ERY, MON
141,678 merged peaks

26. Barplot About half the single peaks come from HPC7.
The majority of the peaks found in only 2 datasets are in the datasets with the highest numbers of peaks.

27. CTCF peaks intersected with ccREs
Split Peaks into low(2-4), mid(5-12) and high (13-15) and find overlaps with ccREs
14,315 / 38,794 = .37
18,600 / 26,880 = .69
12,836 / 13,158 = .98
CTCF peaks found in many cell types are very likely to also be ccREs.
CTCF peaks intersected with ccREs

28. Most common pattern is all cell types
Most common if only 1 missing is cells with fewest peaks
If only 2 missing it is most often MON, then G1E, and CH12
Most common 4 missing is MON + G1E
Most common pattern with less than ½ the cells include the cells with the greatest numbers of peaks
Both ERY, HPC7, TCD4, TCD8
Looking at ones found in both ERY and ER4, the most common patterns are all or nearly all cell types
Patterns in replicated peaks (47,961) are dominated by peak counts in the cell types

29. CTCF peaks and IDEAS states
Out of 141, 678 peaks
50,641 are in state 0 in nearly all used cell types (quiescent)
4,653 are in state 1in nearly all used cell types (transcribed)
Other frequently seen and conserved states are
7 (CTCF), 2 (heterochromatin), 10 (active promoter-like), 15(promoter-like)
Leaving 81,421 peaks with mixed states
CTCF peaks and IDEAS states

30. Counts of peaks in conserved states

31. State 7 peaks State 7 (CTCF) peaks are called in most datasets
Found 1,714 peaks with min 3 and max 15
average 12.4
median 13
first quartile 11
third quartile 15
State 7 peaks

32. State 0 peaks State 0 peaks are mostly found in few datasets
Found 50,641 peaks with min 1 and max 15
average 3
median 1
first quartile 1
third quartile 3
State 0 peaks