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This article mainly introduces the use of the Cistrome DB 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.

The goal of Cistrome is to provide a comprehensive database for genome cis-acting element analysis. By collecting chip_seq, DNase_seq, ATAC_seq raw data from GEO,ENCODE and other public databases, using a unified analysis method, comparing reference genomes with bwa, and then using macs2 for peak calling, the analysis results are integrated into an online database. The construction process and functional modules of the whole database are shown below.

The web address is as follows

Http://cistrome.org/db/

The relevant data of humans and mice included in the database are summarized as follows.

In terms of quantity, cistrome can be said to be the database with the largest number of chip types.

Through the search tool on the home page, we can view the results of specific data analysis, either by keyword search, or by species, sources, and factor types step by step, as shown below

Check the data set you are interested in in the search results to view the details. Take the chip data of a CTCF transcription factor as an example, the result contains the following parts

1. QC report

The QC of the data, including the proportion of unique mapping, the distribution proportion of PBC, FRiP and peak in exon and other genomic regions, is shown below.

2. Motif

The results of motif analysis are as follows

Click the number of each motif to view the details, as shown below

3. Putative target gene

Potential target genes, as shown below

At the same time, you can also view the distribution of the data in the genome browser, or download the result file of the analysis, as shown below

The ToolKit menu provides a richer range of analysis tools, as follows

Enter the name of the gene to see which transcription factors may regulate the gene

Enter the genome region to see which transcription factors may bind to that region

Enter the peak results to see which transcription factors have obvious overlap with your input results, which can be used for colocation analysis of transcription factors.

Take the first function as an example, enter the gene, determine the upstream and downstream range of TSS as the potential regulatory region, and then submit it for operation.

In addition to the results in table format, it also provides a graphical representation of the results, as shown below

Thank you for reading this article carefully. I hope the article "what's the use of Cistrome DB 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!

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