Shulou(Shulou.com)06/01 Report--

This article mainly introduces the use of the TRRUST database, has a certain reference value, interested friends can refer to, I hope you can learn a lot after reading this article, the following let the editor take you to understand it.

TRRUST database is a database that records the regulatory relationship of transcription factors, which contains not only the target genes corresponding to transcription factors, but also the regulatory relationships between transcription factors. At present, the database only stores the regulatory information related to humans and mice, and these regulatory relationships are sorted out from the literature by the method of text mining.

The latest version of the database is v2, and the URL is as follows

Http://www.grnpedia.org/trrust/

For human, it contains 8444 transcriptional factors and 8444 regulatory pairs; for mouse, it contains 828 transcriptional factors and 6552 regulatory pairs.

The official website provides a list of human and mouse transcription factors. In the case of human, the link to the list of transcription factors is as follows

Http://www.grnpedia.org/trrust/data/search_list.human.htm

The corresponding gene symbol, Entrez ID and other information of each transcription factor are given, which can be used for retrieval.

Through the query function of the official website, we can query not only the target gene targets of the transcription factor, but also other transcription factors that regulate the transcription factor, namely regulators, as shown below

Enter the corresponding gene symbol in the search box, and that's fine. If the input gene is the corresponding gene of a transcription factor, it will output both the target gene of the transcription factor and other transcription factors that regulate the transcription factor, as well as the functional annotations related to the gene, such as GO, KEGG, etc.; if the input gene is not a transcription factor, it will only output the transcription factor that regulates the gene.

Taking the transcription factor AHR as an example, the search results include the following sections

1. Target genes corresponding to transcription factors

two。 Other transcription factors that regulate the transcription factor

3. Other transcription factors with the same target genes as AHR

4. Functional or disease notes related to the imported gene

Contains three kinds of annotation information: Disease Ontology, Gene Ontology and KEGG pathway.

In addition to the query function, the database also provides a function to find key TF, as shown below

Input a series of genes, such as the differential genes obtained by differential analysis, through Fisher's accurate test, analyze which transcription factors are enriched, the results are as follows

The database can be downloaded for free and provided in tsv format, which is convenient and intuitive. The schematic diagram is as follows.

Thank you for reading this article carefully. I hope the article "what's the use of TRRUST database" shared by the editor will be helpful to you? at the same time, I also hope you will support us and pay attention to the industry information channel. More related knowledge is waiting for you to learn!

Welcome to subscribe "Shulou Technology Information " to get latest news, interesting things and hot topics in the IT industry, and controls the hottest and latest Internet news, technology news and IT industry trends.