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

There are two common methods to study the target genes regulated by transcription factors. the first is to use chip-seq to study the binding position of specific transcription factors in the genome, so as to determine the regulatory genes. Because of the support of experimental evidence, the regulatory genes obtained in this way will be more credible, and the problem is the false positive rate of peak calling.

Another way is that under the condition that the motif of the transcription factor is known, software such as FIMO can be used to find the promoter sequence of the gene. If it can match, it shows that the gene may be the target gene. This way is simply to predict the target gene by means of calculation. Relatively speaking, the false positive rate will be higher.

TFTG database, whose full name is Transcription Factor Target Gene Databse, is a database of transcription factor target genes. The database combines experimental and analytical methods to study the regulatory relationship between transcription factors and target genes. The diagram is as follows.

For transcription factor USF1, its motif is known. First, the FIMO software is used to find the corresponding motif in the gene promoter, where the promoter region is defined as the upstream and downstream 5KB of the transcriptional initiation site TSS. In this way, three candidate transcription factor binding sites TFBS are found.

Then, according to the results of DNAse-seq, the third site can be excluded because its chromatin is not open, and then according to the results of DGF blotting, the first site is excluded and there is no imprinting at this site. Finally, combined with the results of the chip-seq experiment of the transcription factor, it can be determined that the second candidate site is a real TFBS.

The database makes comprehensive use of the above experiments and analysis methods, and finally constructs a highly reliable transcription factor target gene regulation data set. Through the search function of the official website, you can view the regulatory network of a gene or transcription factor.

For transcription factors, take TP53_MA0106.1 as an example, the search results contain the following information

1. Sequence logo

two。 Target genes corresponding to transcription factors

For genes, take AACS as an example, the search results contain the following information

1. Basic information

2. TFBS

The database is downloaded free of charge and provides the following two types of data

In the excel file, the names of all transcription factors are saved, and the corresponding genetic information is shown below.

What is saved in the compressed file is the target gene information corresponding to each transcription factor. Through this database, we can not only get the target gene information corresponding to transcription factors, but also learn from its ideas to solve the problem, comprehensive experimental means and calculation methods to reduce the false positive rate.

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