Skip to main content

Table 1 Statistics of ChIA-PET data analysis

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

  IHH015Aa IHH015Mb IHH015Cc
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, filteredd) 5223 4,035 24
Intra-chromosomal interactions (FDR <0.05; PET cluster size ≥ 3; filteredd) 2221 1,945 12
Inter-chromosomal interactions (FDR <0.05; PET cluster size ≥ 3; filteredd) 18 12 0
  1. 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.