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This article will explain in detail what database mutagene is. Xiaobian thinks it is quite practical, so share it with you for reference. I hope you can gain something after reading this article.

Mutagene is a database of tumor mutation spectrum, which collects somatic mutation data on protein-coding genes from ICGA, TCGA and other tumor projects, and analyzes and identifies corresponding mutation spectrum.

following address

https://www.ncbi.nlm.nih.gov/research/mutagene/

Through the Explore menu, you can view the mutation spectrum information included in the database, including two parts.

1. Mutational profiles

Calculate the mutation spectrum according to the following four conditions

Cancer types

Primary tumor sites

Benign samples

Cancer Census Genes

Taking tumor type as an example, the results are shown as follows

Each mutation spectrum is uniquely identified by a number beginning with MG, providing a histogram of the corresponding frequency distribution, illustrated as follows

2. Mutational signatures

Using NMF non-negative matrix factorization algorithm to extract mutation features from mutation spectrum, the following features are provided

MUTAGENE-5 signatures

MUTAGENE-10 signaltures

COSMIC-30 signatures

results are shown below

Compare allows you to compare different mutation spectra and cluster them according to the mutation spectra of the samples. The results are shown below.

Comparison of multiple mutation spectra, the results are presented as heat maps, and the following four distances are defined to measure the differences between different mutation spectra

Chi-squared distance

Cosine distance

Helliger distance

Jensne-Shannon distance

Detailed calculation formula can refer to the official document. The heat map of multiple spectrum comparisons is shown below.

A comparison of the spectra of mutations, the results contain the following four parts

1. Scatterplot

Scatter plots are used to show the distribution of abrupt frequencies in two spectra. The results are shown as follows

2. Log-ratio plot

Calculate the logarithm of the frequency ratio in the two spectra, greater than 0 means high expression in one group, less than 0 means high expression in the other group, and display the log ratio value in the form of histogram. The result is shown as follows

3. Histograms

Putting the histograms of the two spectra together for comparison, the results are shown below

4. Distance measures

the results are indicated as follows

In addition, the official website also supports uploading VCF files, calculating mutation spectrum and other functions. For more usage, please refer to the help document of the official website.

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