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How to understand the Super Enhancer Database SEdb

2025-01-28 Update From: SLTechnology News&Howtos shulou NAV: SLTechnology News&Howtos > Internet Technology >

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How to understand the super enhancer database SEdb, many novices are not very clear about this, in order to help you solve this problem, the following editor will explain for you in detail, people with this need can come to learn, I hope you can gain something.

Enhancers, as cis-acting elements in the genome, play an important role in the regulatory network. With the deepening of the research, scientists put forward the concept of super-enhancer super-enhancer, which defines the region of the genome rich in enhancers as super-enhancers.

Similar to defining the region rich in CpG sites as CpG island, the idea of defining and studying the region enriching certain elements separately is very common in the field of biology, reflecting the diversity of functional levels of different elements, from a single site to a group of sites, the hierarchy of functional research also corresponds to the complex regulation mechanism of life.

Similar to the study of enhancers, the regulatory role of super enhancers in different biological processes, disease occurrence and development is also studied. SEdb is a comprehensive super enhancer database, which uses the histone modification of H3K27ac as the marker of the enhancer region. Using the H3K27ac chip_seq data downloaded from ENCODE, RoadMap, GEO and other public databases, MACS is preferred to identify the enhancer region, and then the software ROSE is used to identify the super enhancer region.

For the identified super enhancers, use bedtools to make the following comments

SNP locus

Download SNP loci from dbSNP database, use 1000G data to analyze linkage disequilibrium of SNP loci, and download disease-related risk SNP locus information from GWAS Catalog and GWASdb to annotate various SNP loci in the super-enhanced subregion.

DHS

Download and annotate the DNase enzyme hypersensitive region information from UCSC and ENCODE

Enhancers

Download and comment the enhanced subregion information from ENCODE and FANTOM5

TFBS

Download and annotate the information of transcription factor binding sites from UCSC

CRISPR/Case9 target sites

Download and annotate the gene editing site information from UCSC

EQTLs

Download and annotate eQTL-gene relational pairs from GTEx, HaploReg, and PancanQTL databases

Motif change

Download the motif information of transcription factors from TRANSFAC and JASPAR databases, and use the R packet of atSNP to calculate the effect of SNP loci on motif.

In addition to annotating the super enhancer, the target genes of the super enhancer are predicted by six different strategies, and all the annotation information and target gene prediction results can be queried and browsed through database retrieval.

Considering the specificity of super enhancers, all data are analyzed and stored in the form of a single sample, as shown below

Click the sample number to view the super enhancer information of a single sample, starting with the basic information of the sample and the distribution of the super enhancer on different chromosomes, as shown below

Next is a list of super enhancers, as shown below

Click the ID in the first column to view the details

1. Overview

2. Annotation

3. Target gene

4. Enhancer

5. Overlap with super-hancers

In addition to the basic retrieval and browsing functions, the database also provides a lot of online tools, and the data is also open for download.

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