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 \(pl_g\) | Â | Window |
Peak count \(pc_g\) | Â | Nearest gene | |
Peak signal \(ps_g\) | Â | ChromHMM | |
Promoter + HiC: peaks | Peak length \(pl_g\) | Â | Window + HiC |
Promoter + HiChIP: peaks | Peak count \(pc_g\) | Â | Window + HiChIP |
Peak signal \(ps_g\) | Â | ChromHMM | |
Peak length \(pl_g*\) | Â | ||
Peak count \(pc_g*\) | Â | ||
Peak signal \(ps_g*\) | Â | ||
Promoter + HiC: C peaks | Peak length \(pl_g+pl_g*\) | Â | Window + HiC |
Promoter + HiChIP: C peaks | Peak count \(pc_g+pc_g*\) | Â | Window + HiChIP |
Peak signal \(ps_g+ps_g*\) | Â | ChromHMM | |
Promoter: peaks + TFs | Peak length \(pl_g\) | Affinities in promoter DHS \(a_{g,t}\) | Window |
Peak count \(pc_g\) | Â | ChromHMM | |
Peak signal \(ps_g\) | Â | ||
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 \(ps_g\) | Â | ||
Peak length \(pl_g*\) | Â | ||
Peak count \(pc_g*\) | Â | ||
Peak signal \(ps_g*\) | Â |