A web tool for super-enhancer associated regulatory analysis

Introduction



We designed a novel web server, SEanalysis, which provides a comprehensive super-enhancers regulatory analysis, involving the identification of SE-associated genes, TFs occupying these SEs and the upstream signaling pathways of idenfitied TFs. Users can perform the following SEs-associated analyses in the web server:
I. Pathway downstream analysis.
II. Upstream regulatory analysis.
III. Genomic region annotation.

The current version of SEanalysis contains a total of 331,551 super-enhancers from over 500 types of cells/tissues, 5,042 TF ChIP-seq data generated from these cells/tissues, DNA-binding sequence motifs for 699 TFs as well as 2,880 pathways from ten databases. SEanalysis supports searching by either SEs, samples, TFs, signaling pathways or genes. Furthermore, the complex regulatory networks formed by these factors can be interactively visualized. In addition, we developed a custom genome browser using JBrowse providing more than 6,000 customizable tracks.

Data Statistical Table



Pathway The Number of Sources 10
The Number of Pathways 2880
TF(ChIP-seq) The Number of Sources 5
The Number of TFs 1044
The Number of Samples 5042
TF(Motif) The Number of Sources 6
The Number of TFs 699
The Number of Motifs 3279
SE The Number of Sources 4
The Number of SEs 331551
The Number of Cells/Tissues 542

For publication of results please cite the following article

Qian, F.C.*, Li, X.C.*, Guo, J.C.*, Zhao, J.M., Li, Y.Y., Tang, Z.D., Zhou, L.W., Zhang, J., Bai, X.F., Jiang, Y. et al. (2019) SEanalysis: a web tool for super-enhancer associated regulatory analysis. Nucleic acids research, 47, W248-W255.

Sister Projects


VARAdb: A variation annotation database for human

ATACdb: A comprehensive human chromatin accessibility database

LncSEA: A comprehensive human lncRNA sets resource and enrichment analysis platform

SEDB: The comprehensive human Super-Enhancer database

TRlnc: A comprehensive database of human transcriptional regulation of lncRNAs

TRCirc: A comprehensive database of human transcriptional regulation of circRNAs

KnockTF: A comprehensive human gene expression profile database with knockdown/knockout of transcription factors

ENdb: A manually curated database of experimentally supported enhancers for human and mouse