Fig. 1
From: Integrative prediction of gene expression with chromatin accessibility and conformation data
Assignment of DNase1-seq peaks to genes. The different setups are illustrated for two genes g1 and g2. The colour code of peaks and the border colour of segments indicate to which gene a peak is assigned. Peaks with a striped filling are not assigned to any gene. a In a window-based annotation, peaks are linked to a gene if they are located within a window w centred at the 5′ transcription start site (TSS) of a gene of interest. \(D_{g1,w1}\) denotes the set of all DHSs overlapping window w1 centred around the promoter of gene g1. b Peaks are linked to the nearest gene, defining nearest as the gene with the closest TSS in linear genomic distance. Here, \(D_{g1,n}\) refers to the set of all DHSs linked to gene g1 following the nearest gene approach. c Using HiC or HiChIP, secondary windows \(v_i\) covering the distal regions linked to the TSS are considered in addition to the TSS window. For gene g1, two additional windows, v1 and v2, are considered, yielding the additional peak sets \(D_{g1,v1}\) and \(D_{g1,v2}.\)