SEanalysis 2.0: a comprehensive super-enhancer regulatory network analysis tool for human and mouse

Super-enhancers (SEs) play an essential regulatory role in various biological processes and diseases through their specific interaction with transcription factors (TFs). Here, we present the release of SEanal-ysis 2.0 (http://licpathway.net/SEanalysis), an up-dated version of the SEanalysis web server for the comprehensive analyses of transcriptional regula-tory networks formed by SEs, pathways, TFs, and genes. The current version added mouse SEs and further expanded the scale of human SEs, docu-menting 1 167 518 human SEs from 1739 samples and 550 226 mouse SEs from 931 samples. The SE-related samples in SEanalysis 2.0 were more than five times that in version 1.0, which significantly im-proved the ability of original SE-related network anal-yses (pathway downstream analysis', upstream reg-ulatory analysis' and genomic region annotation') for understanding context-specific gene regulation. Furthermore, we designed two novel analysis mod-els, TF regulatory analysis' and Sample compara-tive analysis' for supporting more comprehensive analyses of SE regulatory networks driven by TFs. Further, the risk SNPs were annotated to the SE re-gions to provide potential SE-related disease/trait in-formation. Hence, we believe that SEanalysis 2.0 has significantly expanded the data and analytical capa-bilities of SEs, which helps researchers in an in-depth understanding of the regulatory mechanisms of SEs. [GRAPHICS] .

Automated summary

SEanalysis 2.0 is a web server for analyzing SE regulatory networks, which has expanded data and analytical capabilities to help researchers gain a deep understanding of the regulatory mechanisms of SEs.