ChIP-seq analysis is started from MACS tool. CEAS then takes peak regions and signal wiggle file to check which chromosome is enriched with binding/modification sites, whether bindings events are significant at gene features like promoters, gene bodies, exons, introns or UTRs, and the signal aggregation at gene transcription start/end sites or meta-gene bodies (average all genes). Then peaks are investigated in these ways: 1. to check which genes are nearby so can be regarded as potential regulated genes, then perform GO analysis; 2. to check the conservation scores at the binding sites;3 the DNA motifs at binding sites.
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