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This article mainly introduces the use of the chipBase 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.

Transcriptional regulation is an important regulatory mechanism in life activities. Through chip_seq data, we can get the regulatory relationship between transcriptional factors or histone modifications and genes. The chipBase database collected more than 10, 000 chip_seq samples from 10 species and sorted out the regulatory networks between transcription factors and various genes, including protein coding genes, lncRNA,miRNA, tRNA and other ncRNA. The database website is as follows

Http://rna.sysu.edu.cn/chipbase/index.php

This data provides not only the regulatory network of transcription factors and various genes, but also the information of transcription factor binding sites and motif. At the same time, the co-expression relationship between transcription factors and genes is analyzed by using the RNA_seq data in TCGA database. The construction process of the whole database is as follows.

There are two types of chip_seq data, one is transcription factor, the other is histone modification. From the data of chip_seq, the region of binding site can be analyzed, which is called peak.

Through the transcription factor binding site, we can further analyze the motif of the binding region, and through the gene annotation of the peak region, we can get the regulatory relationship between transcription factors and various genes.

The database divides genes into the following categories

LncRNA

MiRNA

OtherNcRNA

Protein

Each category corresponds to a submenu. Taking LncRNA as an example, the regulatory relationship between a transcription factor and lncRNA can be retrieved. The search box is as follows

Analyzing the regulatory relationship between transcription factors and genes through chip_seq data is actually obtained by annotating the peak region. Because the binding site is located near the gene, it is usually designated a region, such as upstream and downstream extension 1kb. If the two regions overlap, it is considered that there is a regulatory relationship between the two.

The search results are as follows, showing all the possible lncRNA regulated by the transcription factor CTCF.

Through the Regulator menu, you can retrieve all the transcription factors that regulate a gene. Take TP53 as an example, the search results are as follows

From the Motif menu, you can view the results of the transcription factor motif analysis, which is shown below

In addition, the official website also provides the following two tools

1. ChIP-Function

All the target genes regulated by transcription factors were analyzed by GO enrichment analysis, and the results are as follows.

2. Co_Expression

Using the expression profile data of about 2000 RNA_seq collated from TCGA and other public databases, the co-expression relationship of specified genes was analyzed. The results are as follows.

The correlation between the expression of two genes was analyzed by calculating pearson correlation coefficient and linear regression, and the results shown below are given.

Through the chipBase database, we can easily check the regulatory relationship between transcription factors and various genes.

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