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This article will explain in detail how to use the HEDD database. The editor thinks it is very practical, so I share it for you as a reference. I hope you can get something after reading this article.

As an important cis-acting element of the genome, enhancers play an important role in transcriptional regulation and participate in many biological processes, including the occurrence and development of diseases.

HEDD is a database of human enhancers and diseases, which collates enhancers identified in ENCODE, FANTOM and RoadMap projects, and establishes the relationship between enhancers and diseases through the regulatory relationship between enhancers and target genes and the relationship between target genes and diseases.

The web address of the database is as follows

Http://zdzlab.einstein.yu.edu/1/hedd.php

At present, a total of 2793316 enhancers are included, including 2328833 enhancers predicted by ChromHMM in the RoadMap project, 65359 enhancers predicted by CAGE sequencing analysis in the FANTOM5 project, and 399124 enhancers predicted by both Segway and ChromHMM in the ENCODE project, as shown below

The various elements contained in the enhancer genome region are annotated, and the following five basic annotation information is provided.

DHS

Annotation of DNase enzyme hypersensitive site

TFBS

Transcription factor binding site annotation

Histone modification

Histone modification notes

Repeats

Notes for repeating component

Conservation

Notes on conservatism among species

Using the target gene of enhancer, the association between enhancer and disease is constructed from the following two angles.

Obtaining the association information between genes and diseases from MalaCards,DISEASES,DisGeNET disease database

Obtaining the association information between SNP loci and diseases from GWAS Catalog,GWASdb,CADD database

The association network between enhancer and disease was constructed by bridging the target gene and the SNP site within the target gene.

Through the Search menu, you can search by genome region, disease name, and target gene information. The search box is shown below.

The search results are as follows

Click the enhancer ID in the first column to view and download details

1. Basic comment

two。 An association with disease

3. Regulatory network between enhancers

4. Regulatory networks among enhancers, genes, and transcription factors

The information in this database can be downloaded free of charge. different from other enhancer databases, HEDD not only provides basic annotation information such as the genome region of enhancers, but also further establishes a regulatory network between enhancers and diseases through target genes, which is of great reference significance for the study of enhancers in diseases.

This is the end of the article on "how to use HEDD database". I hope the above content can be helpful to you, so that you can learn more knowledge. if you think the article is good, please share it for more people to see.

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