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.
|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|
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.
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