Skip to main content

Table 1 Different combinations of features evaluated in this study

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

Name Considered peak features Considered TF features Annotation
Promoter: peaks Peak length \(pl_g\)   Window
Peak count \(pc_g\)   Nearest gene
Peak signal \(ps_g\)   ChromHMM
Promoter + HiC: peaks Peak length \(pl_g\)   Window + HiC
Promoter + HiChIP: peaks Peak 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 peaks Peak length \(pl_g+pl_g*\)   Window + HiC
Promoter + HiChIP: C peaks Peak count \(pc_g+pc_g*\)   Window + HiChIP
Peak signal \(ps_g+ps_g*\)   ChromHMM
Promoter: peaks + TFs Peak 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 \(ps_g*\)