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This article mainly shows you "what is the use of 3DIV database", the content is easy to understand, clear, hope to help you solve your doubts, the following let the editor lead you to study and learn "what is the use of 3DIV database" this article.

The full name of 3DIV is as follows

3D-genome Interaction Viewer and databse

Is a database of chromatin spatial interaction. Through this database, you can query all chromatin fragment information that interacts with a chromatin region of interest. It is a query mode of one-to-all.

The website of the database is as follows

Http://kobic.kr/3div/

The information of chromatin interaction was obtained by downloading Hi-C raw data from GEO and other public databases for analysis. For chromatin regions, the following three types of annotation information are further provided

Gene annotation

Gwas snp annotaion

Chip singal annotation

All the information stored in the database is shown in the following figure

For the specific chromatin region input, firstly, the chromatin region that interacts with it in the hi-c map is recorded, and then the signal distribution of various histone modifications in this region, the corresponding genes and disease-related snp sites located in this region are provided.

The query function of the database is divided into three modules shown in the following figure.

1. Interaction Table

This module is used to query the interaction information of a chromatin region, and supports input of chromatin region, gene name and rs number. The query results are as follows

Output the bin regions in a specific sample that interact with the query region, and give the corresponding distance, as well as the interaction frequency before and after normalization, and other subsequent annotations corresponding to the bin region.

2. Interaction visualization

This module is used to view the hi-C map of a specified area, and the results are as follows

The blue triangle represents the topological association domain TAD, the middle part is the interaction frequency between the input region and other bin, the blue column is the original frequency, and the pink scatter is the corrected interaction frequency, in which the green horizontal line is the filtering threshold, and the two interaction chromatin regions greater than this threshold are connected by the lowest curve.

3. Comparative interaction visualization

This module is used to compare chromatin interaction information in multiple samples, and the results are as follows

You can see that different samples are represented in red and blue in the vs information bar, while the corresponding blue and red in the Hi-C map, where the blue region represents the high interaction frequency of the region in the blue sample, and the red region represents the high interaction frequency in the red sample. The meaning of the following figure is the same as in the module II.

Through this database, the chromatin interaction information based on hi-c data can be retrieved and viewed.

The above is all the contents of the article "what is the use of 3DIV database". Thank you for reading! I believe we all have a certain understanding, hope to share the content to help you, if you want to learn more knowledge, welcome to follow the industry information channel!

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