Fig. 2: Conceptual framework of the SE-to-gene Links analysis and network mapping.
From: SEgene identifies links between super enhancers and gene expression across cell types
a Identifying SE-associated peaks: Peaks within a predefined search window that show significant correlations with specific genes are identified using P2GL analysis. SEs containing these correlated peaks are then selected for further analysis. b Merging SE regions across samples: SE regions identified in multiple samples are consolidated to form a unified region, referred to as a “Merged SE”. This consensus SE region represents data integrated across all samples. c Building a multi-layer network: In the same chromosomal region, the genes identified through P2GL analysis, their associated peaks, and the corresponding merged SE are mapped as shown in the upper section. These components are represented as nodes in a three-layer network as illustrated in the bottom section.
