SEgene

SEgene identifies links between super enhancers and gene expression across cell types using the peak-to-gene links approach to reveal correlations between genes and peak regions.

Key Features:

• Peak-to-gene links approach: A statistical method that reveals correlations between genes and peak regions to evaluate super-enhancer regions in relation to gene expression.
• Super-enhancer detection: Accurately detects super-enhancers from histone mark chromatin immunoprecipitation followed by sequencing data and identifies their functionally associated genes.
• Targeted evaluation: Facilitates identification of super-enhancers functionally linked to transcriptional activity for evaluation as potential therapeutic targets.

Scientific Applications:

• Cancer research: Identifies clinically significant super-enhancer regions and functionally associated genes in cancer datasets, such as ERBB2 in lung adenocarcinoma.
• Therapeutic target evaluation: Supports evaluation of super-enhancers as potential therapeutic targets through identification of their linked genes.
• Cross-cell-type analysis: Enables comparison of super-enhancer to gene links across different cell types using public datasets.

Methodology:

SEgene incorporates the peak-to-gene links approach, a statistical method designed to reveal correlations between genes and peak regions. The SE-to-gene Links analysis was applied to public datasets including the National Cancer Center Japan cohort lung adenocarcinoma dataset.