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This article mainly shows you "what is the use of DENdb 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 DENdb database" this article.

DENdb uses five different methods to predict enhancers in different human cell lines, and also provides overlap information on enhancer subregions, DNA endonuclease hypersensitive sites and transcription factor binding regions.

Http://www.cbrc.kaust.edu.sa/dendb/index.php

The five methods used are listed below

ChromHMM

Segway

RFECS

CSI-ANN

ENCODE integrated annotation

The number of enhancers predicted by different cell lines in the database is summarized as follows

The number of enhancers corresponding to each method is as follows

At present, the retrieval function of the database has been invalidated. We can only view the information about enhancers from the downloaded files. From the downloaded enhancers.csv.zip files, we can view the interval information of enhancers in each cell line. Some of the contents of the files are shown below.

The hypersensitive sites of DNAse enzyme identified by DNAse_seq can be obtained from the downloaded dnase.csv.zip file. Some of the contents of the file are as follows.

From the downloaded enhancer_dnase.csv file, the intersection information of enhancer and DNase enzyme hypersensitive site can be obtained. Some of the contents of the file are as follows.

Similarly, the information of TFBS and the intersection of enhancer and TFBS can be obtained from the download file, and the enhancer target gene information is also provided. This information can be obtained according to the enhancer_targets.tsv.zip file, and some of the contents of the file are shown below.

The enhancer interval information in this database is located based on the hg19 version of the genome, and its method of predicting the enhancer interval should be used for reference.

The above is all the contents of the article "what is the use of DENdb 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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