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This article mainly explains "how to use GREAT for functional comments on peak", the content of the article is simple and clear, easy to learn and understand, the following please follow the editor's ideas slowly in-depth, together to study and learn "how to use GREAT for functional annotations of peak" bar!

GREAT is a tool for gene annotation in the peak region, which not only gives the corresponding genes of peak, but also integrates the functional analysis of a variety of genes.

Http://great.stanford.edu/public/html/index.php

Currently, the online tool only supports the following species

Human

Mouse

Zebrafish

When using it, you also need to pay attention to the corresponding version of the genome. The usage is relatively simple. Select the corresponding genome version, and then upload the corresponding peak file in BED format, as shown below.

The results are shown as follows, and the frequency distribution histogram of the number of peak-associated genes and TSS distance is given.

In addition, the functional analysis of the following genes is also given.

GO Molecular Function

GO Biological Process

GO Cellular Component

Mouse Phenotype

Human Phenotype

Disease Ontology

MsigDB Cancer neighborhood

Placenta Disorders

PANTHER Pathway

BioCyc Pathway

MsigDB Pathway

MGI Expression

MgisDB Perturbation

Different from the traditional Fisher exact test, the p value of functional enrichment analysis is calculated based on binomial distribution. The calculation process is as follows.

Take the functional notes for the category MF in GO as an example, as shown below

Through GREAT, it is convenient to explore the function of genes associated with peak.

Thank you for your reading, the above is the content of "how to use GREAT for functional annotation of peak". After the study of this article, I believe you have a deeper understanding of how to use GREAT to annotate the function of peak, and the specific use needs to be verified in practice. Here is, the editor will push for you more related knowledge points of the article, welcome to follow!

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