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This article mainly shows you "how to use FANTOM5 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 "how to use FANTOM5 database" this article.

The full name of FANTOM is as follows

Function Annotation Of The Mammalian Genome

Is an international research project, founded in 2000, the original purpose is to functional annotation of mouse full-length cDNA sequence. With the continuous development, the content of the research is also expanding at the transcriptology level.

In the third phase of the project, CAGE-seq was used to accurately study the transcriptional initiation site TSS of different transcripts, as shown below

CAGE technique can be used to distinguish the initiation sites of different transcriptional isoforms. Based on the accurate TSS site, the transcriptional regulatory regions such as promoters and enhancers were further studied and analyzed.

In addition to conventional protein-coding genes and transcriptional regulation, the project has also been studied in the field of lncRNA, miRNA and other non-coding RNA, namely ncRNA. The relevant results and data are open to the world and can be downloaded from the official website.

What we are going to introduce today is the enhanced data obtained from the project, which can be found at the following URL

Http://slidebase.binf.ku.dk/human_enhancers/

Through Human Enhancer Selector. The enhanced sub-data can be retrieved as follows

The search result is divided into two parts. The genome location of the enhancer can be seen on the left side of the page. You can download files in BED and FASTA formats, or you can query the corresponding motif analysis results, as shown below.

On the right side of the page, the expression level of enhancers is given, which is divided into the following three levels

Cell

Organ

Sample

Corresponding to the expression level of different cells, organs and samples, take the expression at the cell level as an example, as shown below

From the View Overlaps menu, you can view the promoter region associated with the enhancer and the SNP sites within the enhancer region, as shown below

Through the above URL, the enhancer can be found and analyzed online. Information about all enhancers can be downloaded from the following link

Interval files in BED format are available for download.

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