Figure 2

Different scenarios for the integration of peaks with gene features. (a) The peaks from a transcription factor (TF) track can be located in the promoter region or 5′ flanking region (peak 1) of gene A, in the coding region (peaks 2 and 3) or in the 3′ flanking region of gene A (peak 4). Peak 4 is at the same time located in the 5′ flanking region/promoter region of gene B. Its association is therefore not strictly clear, which should be considered during peak annotation. (b) The peaks of two transcriptional regulators (two TFs, two Histone Modifications (HMs), or a TF and a HM, etc.) can be integrated based on their overlapping or nearby location in different attributes of a gene feature, as here demonstrated by their common overlap with the promoter region of a gene. (c,d) Activity of a transcriptional regulator, such as an enhancer, is not necessarily linked to the closest gene, but could affect neighbouring genes up- or downstream of the peak. Data from a differential expression analysis (DEA) of nearby genes can be correlated with a genomic peak harbouring a non-coding mutation or a genomic region harbouring a genome deletion. Long-range interactions can also be determined by specific genomic boundaries defining so-called TAD-domains (topologically associating domains).