Intersect/Summarize FCC peak calls by accessible regions

STARR/MPRA

After intersect all STARR/MPRA peak calls with ATAC regions, we could summarized ATAC reigon count table as follow:

Group	Peak (Total)	ATAC (Overlap)	ATAC (Union)
ASTARR	229,239	90,765	121,822
LMPRA	26,192	20,905	22,274
TMPRA	6,329	848	1,106
WSTARR	165,627	29,329	38,048

There are 99,749/135,016 ATAC regions intersected with at least one STARR/MPRA peak.

Distribution of GC content and region length at ATAC region; splitted by active and repressive peaks for each reporter assay

Summarize by direction:

Some regions may contain only active

Region	Group	Active	Active:Repressive	Repressive
fcc_astarr_macs_input_overlap	ASTARR	17,042	9,119	64,604
fcc_astarr_macs_input_overlap	LMPRA	20,660	32	213
fcc_astarr_macs_input_overlap	TMPRA	835	12	1
fcc_astarr_macs_input_overlap	WSTARR	26,140	852	2,337
fcc_astarr_macs_input_union	ASTARR	18,245	11,381	92,196
fcc_astarr_macs_input_union	LMPRA	21,985	37	252
fcc_astarr_macs_input_union	TMPRA	1,082	21	3
fcc_astarr_macs_input_union	WSTARR	31,974	1,376	4,698

Total number of CASA peaks across 20 genes

There are 102 CASA peaks across 20 genes. After summarized using ATAC regions, about 80 ATAC regions contain at least one CASA peak.

Group	Peak (Total)	ATAC (Overlap)	ATAC (Union)
CRISPRi-HCRFF	102	84	86

Some regions regulate multiple genes. For example,

Total DHS contains significant guides: 6,242

Group	Peak (Total)	ATAC (Overlap)	ATAC (Union)
CRISPRi-Growth	6,242	4,380	4,907

The results showed that 4k ATAC regions containing at least one significant guides.

A few regions contains more than one since ATAC peaks tends to have longer length than DHS peaks.

Number of links

Group	Link (Total)	ATAC (Overlap)	ATAC (Union)
E2G-Benchmark	472	422	424

Number of regions

Group	Peak (Total)	ATAC (Overlap)	ATAC (Union)
E2G-Benchmark	420	360	362

Using the ATAC region, we could summarise the regions that regulate multiple genes.

Pairs that are also captured in CRISPRi-HCR FlowFISH

score distribution