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Table 1 Different combinations of features evaluated in this study

From: Integrative prediction of gene expression with chromatin accessibility and conformation data

NameConsidered peak featuresConsidered TF featuresAnnotation
Promoter: peaksPeak length \(pl_g\) Window
Peak count \(pc_g\) Nearest gene
Peak signal \(ps_g\) ChromHMM
Promoter + HiC: peaksPeak length \(pl_g\) Window + HiC
Promoter + HiChIP: peaksPeak count \(pc_g\) Window + HiChIP
Peak signal \(ps_g\) ChromHMM
Peak length \(pl_g*\) 
Peak count \(pc_g*\) 
Peak signal \(ps_g*\) 
Promoter + HiC: C peaksPeak length \(pl_g+pl_g*\) Window + HiC
Promoter + HiChIP: C peaksPeak count \(pc_g+pc_g*\) Window + HiChIP
Peak signal \(ps_g+ps_g*\) ChromHMM
Promoter: peaks + TFsPeak length \(pl_g\)Affinities in promoter DHS \(a_{g,t}\)Window
Peak count \(pc_g\) ChromHMM
Peak signal \(ps_g\) 
Promoter + HiChIP: peaks + TFs (EF)Peak length \(pl_g\)Affinities in promoter DHS \(a_{g,t}\)Window + HiChIP
Peak count \(pc_g\)Affinities in loop DHS \(a_{g,t}*\)ChromHMM
Peak signal \(ps_g\) 
Peak length \(pl_g*\) 
Peak count \(pc_g*\) 
Peak signal \(ps_g*\)