ChIA-PET tool for comprehensive chromatin interaction analysis with paired-end tag sequencing

Table 1 Statistics of ChIA-PET data analysis

	IHH015A^a	IHH015M^b	IHH015C^c
Total PETs	13,866,893	4,269,610 (30.8% of IHH015A)	6,157,038 (44.4% of IHH015A)
Unique PETs with unique mapping	3,826,699	1,501,442	1,710,335
Self-ligation PETs	611,622	491,750	12,155
Different orientation PETs	31,543	24,960	548
Intra-chromosomal inter-ligation PETs (excludes different orientation PETs)	223,170	91,519	94,743
Inter-chromosomal inter-ligation PETs	2,960,364	893,213	1,602,889
Binding sites (FDR <0.01, filtered^d)	5223	4,035	24
Intra-chromosomal interactions (FDR <0.05; PET cluster size ≥ 3; filtered^d)	2221	1,945	12
Inter-chromosomal interactions (FDR <0.05; PET cluster size ≥ 3; filtered^d)	18	12	0

^aThe original ChIA-PET dataset without linker filtering. ^bThe dataset containing non-chimeric linker compositions AA and BB. ^cThe dataset containing chimeric linker composition AB, considered as non-specific proximity ligation noise. ^dThe binding sites and interactions after filtering those from chromosome Y, the mitochondria, and satellite repeat regions, and interactions from genome structural variations in the MCF-7 cell-line. FDR, false discovery rate.

ISSN: 1474-760X