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ChIP-Atlas is based on how to analyze and mine public data. For this problem, this article introduces the corresponding analysis and solution in detail, hoping to help more small partners who want to solve this problem find a simpler and easier way.

ChIP-Atlas collects and organizes a large amount of chip_seq data in SRA database, and performs subsequent analysis based on these raw data. The analysis results are organized into online services and published for easy retrieval and query/query.

The process of construction is as follows

Download SRA raw data, convert to fastq using sratokit, align reference genome with bowtie2, and perform peak calling with macs2. The website provides the following functions

1. Peak Browser

Browse peak results of different species, different cell types and different antibodies. The search box is shown as follows

The results can be downloaded in BED format.

2. Target genes

The upstream and downstream intervals of TSS are defined as the screening range of target genes. If peak intersects with both sides of TSS of a gene, the gene is considered as one of the candidate target genes. The search box looks like this

The search results are as follows

3. Colocalization

Some transcription factors function in the form of protein complexes, such as Pu 5f1, Nanog, Sox2, these three transcription factors, their corresponding peak interval in the gene position is very close, Colocalization analysis is to compare the chip data of multiple transcription factors, to identify potential protein complexes, the search box is as follows

The search results are as follows

4. Enrichment Analysis

As opposed to target gene analysis, the target gene is the name of the input transcription factor, and the query predicts the target gene, and this part of the content is the name of the input gene or the genome region, and the query can bind to the transcription factor. The search box is as follows

the results are indicated as follows

Through the Chip Atlas website, you can easily query the existing chip_seq data results.

About ChIP-Atlas based on public data how to analyze mining questions to share here, I hope the above content can be of some help to everyone, if you still have a lot of doubts not solved, you can pay attention to the industry information channel to learn more related knowledge.

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