Fig. 8

Distributions of genomic features in different replication phases and genomic zones. a Levels of various genomic features (as shown on x-axis) within all 1-kb windows (upper panel), all hotspots (middle panel), or all clusters (lower panel) belonging to replication phases G1b-G2 in the Genic (G), Proximal (P), or Distal (D) zones, in accordance to the red-blue thermal scale for fold-change over autosomal average (see Supplementary Table S10 for data on genomic-feature enrichments). b Enrichment map for Distal-zone genes annotated using g:Profiler [71] based on Gene Ontology biological process [72] and KEGG [73]. Each node represents a pathway (with 3 to 350 genes) significantly enriched in Distal zones with Benjamini-Hochberg false discovery rate < 0.05, and node size is proportional to the number of Distal-zone genes belonging to the pathway (see pathway IDs in Supplementary Figure S11). Pathways are connected by a gray edge when they share ≥ 50% genes. Node color, represented by the red-blue thermal scale, indicates the fold-change of the fraction of the genes over the fraction of 1-kb sequence windows that overlap with hotspots in the Distal-zone S4 and G2 phase DNA (see Supplementary Table S11). Asterisks mark pathways that overlap with cluster(s). c Selection status of pathway genes that overlap with hotspots in the Distal-zone S4 and G2 phases. Fractions of genes overlap only with PosSel-Hs (red slices), with both PosSel-Hs and NegSel-Hs (purple slices), and with all (black slices) or none (beige slices) of PosSel-Hs, NegSel-Hs, and BalSel-Hs