Gene

Enhancer

Genome

Gene expression

Regulation of gene expression

Genomics

Cis-regulatory module

Regulatory sequence

Genome browser

Computer science

Genetics

Gene regulatory network

Computational biology

Database

Transcription factor

Biology

Nucleic Acids Research

Super-enhancers (SEs) have prominent roles in biological and pathological processes through their unique transcriptional regulatory capability. To date, several SE databases have been developed by us and others. However, these existing databases do not provide downstream or upstream regulatory analyses of SEs. Pathways, transcription factors (TFs), SEs, and SE-associated genes form complex regulatory networks. Therefore, we designed a novel web server, SEanalysis, which provides comprehensive SE-associated regulatory network analyses. SEanalysis characterizes SE-associated genes, TFs binding to target SEs, and their upstream pathways. The current version of SEanalysis contains more than 330 000 SEs from more than 540 types of cells/tissues, 5042 TF ChIP-seq data generated from these cells/tissues, DNA-binding sequence motifs for ∼700 human TFs and 2880 pathways from 10 databases. SEanalysis supports searching by either SEs, samples, TFs, pathways or genes. The complex regulatory networks formed by these factors can be interactively visualized. In addition, we developed a customizable genome browser containing &gt;6000 customizable tracks for visualization. The server is freely available at http://licpathway.net/SEanalysis.

SEanalysis: a web tool for super-enhancer associated regulatory analysis