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.

Li et al. Genome Biology 2010 11:R22   doi:10.1186/gb-2010-11-2-r22