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This article mainly introduces the example analysis of peak annotation information in chip_seq data analysis, which has a certain reference value, and interested friends can refer to it. I hope you can learn a lot after reading this article.

In chip_seq data analysis, peak calling is the core. After we get the peak interval, we first need to annotate the peak. The so-called annotation is actually a relatively broad concept, which contains the following various types of annotation information

1. Enrichment profile

Profile is a high-frequency word in bioinformatics analysis, which has different meanings in different genomic data. Here, it represents the distribution of reads in the peak region on the genome. The most basic annotation is to look at the distribution of reads in the peak region on each chromosome, as shown below

Enrichment stands for enrichment, which is specific to a characteristic site, such as the most common distribution of peak reads on both sides of the transcriptional initiation site, as shown below

The line chart reflects the distribution of reads in the peak region on all transcripts. In order to represent all transcripts as one value, the average value is usually taken. There is also a way to display a heat map, with each line representing an transcript, as shown below

In addition to the distribution of a single locus such as TSS, it can also show the distribution across the entire genome, as shown below

2. Genome location annotation

This kind of annotation mainly analyzes the overlap of peak interval and various regions of the genome, such as 5 regions UTRJO 3 regions UTR, exon, etc., and then draws pie charts or bar charts, as shown below.

The division of genomic regions varies according to the annotation file.

3. Gene annotation

This part of the annotation mainly analyzes the relationship between peak interval and genes, which can be subdivided into two types: overlap gene and nearest non-ovlap gene. The first analysis determines which gene regions the peak interval is located in, as shown below

The second analysis of genes with no intersection in the nearest upstream and downstream interval of peak is shown as follows

The reason why gene annotation is made is to explore the target genes modified by transcription factors or histone. At present, there is no unified view on the screening strategy of target genes. The genes selected by the above two annotations can be used as candidate target genes, and then carry out functional enrichment analysis such as GO/KEGG.

Thank you for reading this article carefully. I hope the article "sample Analysis of peak Annotation Information in chip_seq data Analysis" 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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