2.4.2. Irreproducible Discovery Rate (IDR)

Irreproducible discovery rate (IDR) was used to verify the consistency between biological replicates within an experiment. The reproducible peaks with an IDR value of 0.05 or less were kept [14]. Motif analysis: The DNA binding site for specific transcription factors or histone modifications was not random, but they showed a conserved DNA sequence pattern. The motifs were detected utilizing the MEME suit. MEME-ChIP was used to scan the motifs reliably through peak regions, and then AME was used to validate the existence of any certain motifs. Differential analysis of multi-samples: The DiffBind was used to analyze peak differences across groups [15]. We identified significantly differential peaks with FDR < 0.05 in two comparison groups. Similarly, genes associated with different peaks were annotated, and the GO functions of enrichment analysis and KEGG pathways were identified.