Region-set comparison

This example compares four classes of accessible HepG2 regions defined by HNF4A and FOXA2 ChIP-seq: HNF4A + FOXA2, HNF4A only, FOXA2 only, and no HNF4A/FOXA2. The last group contains accessible regions overlapping neither ChIP-seq peak set.

The classes were restricted to a shared baseline-accessibility range, divided into 50 strata, and sampled equally within every stratum. Each class contains 4,786 regions. Three HepG2 ATAC-seq replicates are analyzed as paired measurements of the same region classes.

Example command

diff-footprints --comparison-axis regions \
  --signals HepG2_rep1_footprints.bw HepG2_rep2_footprints.bw HepG2_rep3_footprints.bw \
  --sample-names "HepG2 rep 1" "HepG2 rep 2" "HepG2 rep 3" \
  --regions HNF4A_FOXA2.bed HNF4A_only.bed FOXA2_only.bed No_HNF4A_FOXA2.bed \
  --region-labels "HNF4A + FOXA2" "HNF4A only" "FOXA2 only" "No HNF4A/FOXA2" --region-strata-column 4 \
  --genome hg38.fa --motif-db jaspar2026_vertebrates \
  --aggregate-signals HepG2_rep1_corrected.bw HepG2_rep2_corrected.bw HepG2_rep3_corrected.bw \
  --plot-aggregate-motifs MA1494.2 MA0484.3 MA0047.4 MA0148.5 MA0046.3 MA0153.2 MA0102.5 MA0466.4 \
  --default-aggregate-plots 8 --outdir HepG2_region_comparison

The primary effect is the matching-stratum-adjusted difference in region-level footprint score. All 1,019 motifs are tested; the eight specified motifs only set the initial aggregate display. Significance is calculated from paired replicate effects using the empirical-Bayes model.

In the default view, HNF4A/HNF4G and FOXA1/FOXA2 footprints are stronger in co-bound regions. The HNF4A-only versus FOXA2-only view separates the two factor families.

All motif results · matching QC · matching summary · source manifest