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This article mainly introduces the use of TiED database, the article is very detailed, has a certain reference value, interested friends must read it!

TiED is a human enhancer database, which quantifies and analyzes enhancer tables in 10 different tissues, and identifies the tissue specificity of enhancers. The website is as follows

Http://lcbb.swjtu.edu.cn/TiED/

Firstly, the enhancer regions are identified by combining the results of H3K27ac, H3K4me1, H3K4me3 and DHS, and the chip_seq data are downloaded from Roadmap and ENCODE. The genomic regions with higher H3K4me1 modification level and lower H3K4me3 level in the range of DHS, H3K27ac and H3K4me1 peak 2kb are selected as candidate enhancers, and then the enhancers with overlap in 1kb upstream of the protein coding gene TSS site are filtered out to get the final enhancer region.

For the enhanced sub-area, the following annotation information is provided

SNP site annotation

Provides annotations for SNP sites that exist in enhanced subregions

Transcription factor annotation

Annotate the transcription factors that potentially regulate enhancers

Target gene annotation

The protein gene in the upstream and downstream 100kb of the enhancer is defined as the possible target gene of the enhancer.

Tissue-specific annotation of target gene

According to the gene expression information provided by the GTEx project, the expression of the target gene of the enhancer in the 10 tissues shown below was analyzed, and the tissue specificity was calculated.

According to the tissue specificity of the target gene, enhancers are divided into the following three categories.

Specific enhancer

Ubiquitous enhancer

Other enhancer

Specific ehhancer is abbreviated as TS enhancer and ubiquitous enhancer is abbreviated as UE enhancer.

Secondly, combined with the results of CAGE sequencing to identify the RNA corresponding to the enhancer, namely eRNA. If the peak of CAGE sequencing is located in the enhancer region, it indicates that the enhancer transcription produces eRNA.

Through the search box on the front page, the database can be searched according to tissue, transcription factor, gene name or genome location. Taking the Heart organization as an example, the results are as follows

The enhancer number begins with the enh prefix plus number and provides information about genome regions, eRNA annotations, tissue-specific annotations, and so on. Click the enhancer number to view the following details

1. Transcriptional factor

2. SNP

3. Tatget Gene

From the Browser menu, you can view the TF-enhancer-gene regulatory network within an organization, as shown below

The information in the database is downloaded free of charge. through this database, in addition to the basic annotations of the enhancer genome region, we can also obtain the regulatory relationship between transcription factors and enhancers, as well as the regulatory relationship between enhancers and genes.

The above is all the contents of the article "what is the use of TiED database". Thank you for reading! Hope to share the content to help you, more related knowledge, welcome to follow the industry information channel!

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