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This article mainly shows you "how to use dbCoRC database", the content is simple and easy to understand, clear organization, I hope to help you solve doubts, let Xiaobian lead you to study and learn "how to use dbCoRC database" this article.

Hundreds of transcription factors have been identified in humans and mice. It is well known that transcription factors are cell or tissue-specific, and only a small number of transcription factors play regulatory functions in a particular tissue or cell.

Scientists have found that even in specific cells or tissues, the transcription factors that play a role in the regulatory network are different. Among them, some transcription factors are called core transcription factors, which can not only regulate their own target genes, but also regulate each other, thus forming a cross-regulatory loop, the most typical is the regulatory loop composed of NANOG, SOX2, POU5F1/OCT4 transcription factors in embryonic stem cells.

Core transcription factors and their regulatory circuits in certain cells or tissues are called core transcription regulatory circuitry (CRC). The SE region of super enhancer contains many transcription factor binding sites. Some scientists invented CRC Mapper algorithm, which identifies CRC in cells or tissues through transcription factors associated with super enhancer.

dbCoRC is a core promoter database that identifies CRC in different tissues or cells by superenhancer-associated transcription factors. With H3K27ac as the mark of enhancer, chip_seq raw data were downloaded from GEO database, enhancer regions were identified by MACS software, and super enhancers were identified by ROSE software.

After super enhancer is identified, the transcription factor motif information is downloaded from TRANSFAC/MEME database, and motif scan analysis is performed by FIMO software to find transcription factor binding sites in super enhancer region. Using this strategy to find the transcription factor that the super enhancer wants to associate with, and on this basis to identify CRC, the complete pipieline is shown below

The corresponding article was published in Nucleic Acids Research, and the link is as follows

https://academic.oup.com/nar/article/46/D1/D71/4103600

The database can be accessed at the following address:

http://dbcorc.cam-su.org/

Through the Browser menu, you can browse CRC information in each sample, as shown below.

Click on the sample name to view the details. First, the regulatory network composed of core transcription factors in the sample is shown as follows

The second is the super enhancer region corresponding to the core transcription factor, which is shown as follows

Click on the ID of the transcription factor to view the binding sites of the transcription factor in the SE region of other transcription factors, as shown below.

At the same time, the expression information of this transcription factor in different databases such as TCGA is also provided, which is shown as follows

dbCoRC focuses on analyzing the regulatory relationships between transcription factors associated with super enhancer regions. If only super enhancers are analyzed, SEdb database is more recommended.

The above is "dbCORC database how to use" all the contents of this article, thank you for reading! I believe that everyone has a certain understanding, hope to share the content to help everyone, if you still want to learn more knowledge, welcome to pay attention to the industry information channel!

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