How to understand the super enhancer database dbSUPER in humans and mice
In this issue, the editor will bring you how to understand the super enhancer database dbSUPER in humans and mice. The article is rich in content and analyzed and described from a professional point of view. I hope you can get something after reading this article.
DbSUPER is the first work of the Super Enhancer database. The article is published on Nucleic Acids Research with the following link
Https://academic.oup.com/nar/article/44/D1/D164/2502575
The web address of the database is as follows
Http://asntech.org/dbsuper/
The information of super enhancers in humans and mice is collected, and two strategies are used to define enhancers.
Collect published, literature-supported super enhancers from pubMed
Using the H3K27ac chip_seq data downloaded from ENCODE, GEO and other public databases, the MACS is used to identify the peak region, and the negative ninth power peak with p less than 10 is used as the enhancer, and then the software ROSE is used to identify the super enhancer.
For human, based on hg19 version analysis, a total of 69205 super enhancers were collected from 102 different cells / tissues; for mouse, based on mm9 version analysis, a total of 13029 super enhancers information from 25 different cells / tissues were included, as shown below
The genes existing in the upstream and downstream 50kb of the super enhancer are taken as the corresponding target genes, and the target genes of the super enhancer are predicted based on this simple strategy. The pipeline for the entire database construction is as follows
From the Browser menu, you can browse the super enhanced sub-data, as shown below
Click the ID of the Super Enhancer to view the following details
1. Basic information
two。 Associated gene
3. Software parameters
4. Sequence download
5. Included enhancer
In addition to basic retrieval and browsing functions, the database also supports the transmission of super enhancer information to other online tools to facilitate downstream analysis, as shown below
The reads distribution of the super enhancer region can be viewed through the UCSC Genome browser, or it can be sent to Cistrom and GREAT for downstream analysis.
The database only provides basic information such as the chromosome location of the super-enhanced sub-region, and lacks the annotation of other basic functional elements in the super-enhanced sub-region.
This is how to understand the super enhancer database dbSUPER in humans and mice shared by Xiaobian. If you happen to have similar doubts, please refer to the above analysis to understand. If you want to know more about it, you are welcome to follow the industry information channel.
