Shulou(Shulou.com)06/01 Report--

In this issue, the editor will bring you a topic about how to use the ICGC database to find a mutation. The article is rich in content and analyzes and narrates it from a professional point of view. I hope you can get something after reading this article.

How to use ICGC database to find a topic related to mutation

Scientific research hypothesis

There are many types of gene mutations, among which the insertion of nucleotides may affect the coding of gene proteins. Therefore, the study of gene mutation insertion is very important.

For solid tumors, many tumors are in the same environment, such as three tumors in the digestive tract: esophagus, stomach and intestine. For tumors in the same environment, the pathogenesis may be the same.

In summary, we want to study the effect of insertion mutation on digestive tract tumors.

1. Effect of mutation insertion of three tumor genes

Since we are going to study the effects of insertion mutations in three tumors. So the first step is to look at the effects on mutation insertion in different tumors. Here we take esophageal cancer as an example:

1.1 check the results of insertion mutations in esophageal cancer

In the screening column of the ICGC database, we select the esophagus among the sample types in Donors and insert the mutation type in Mutations. In this way, we can find out what genes are associated with insertion mutations in esophageal cancer. After screening, we found that 17552 genes were associated with insertion mutations.

1.2 Analysis of gene characteristics of insertion mutant gene

After knowing the results of insertion mutations associated with esophageal cancer, we can first conduct a simple analysis of these results.

First of all, we can observe the type of mutation through oncoplot.

In addition, we can enrich and analyze these genes with insertion mutations. Observe what function these mutated genes mainly affect.

After a simple analysis of the results, we can save the results of this gene set for subsequent cross-analysis.

By repeating the above screening and analysis steps, we can get the results of insertion mutation-related genes in the three cancer species.

two。 Cross analysis of multiple cancer species

In? In the process of data screening and analysis, we can obtain genetic data sets related to insertion mutations in three different cancer species. At this time, we can cross-analyze the three data sets. To find mutated genes that are associated with all three cancers.

ICGC provides access to cross-analysis. We can use Set Operations in Data Analysis for cross-analysis. Here we select Select and we can select the dataset to intersect.

Select the three datasets we obtained after filtering in Select. Click Run to get the results.

Finally, we can find that 269 gene insertion mutations occur in all three cancers.

We click on 269 of the results to see what all these 269 genes are.

3. Further analysis of the data

After the above analysis, we found that there are 269 gene insertion mutations that affect. But if we study, we can't study all 269 genes. So we have to pick one for research. Of the 269 genes, some are antisense strands of lncRNA. Because lncRNA is also quite popular. So we want to see which lncRNA mutation has an impact on the tumor.

So we choose the antisense chain in the gene type. Finally, it was found that lncRNA with 13 antisense chains was associated with three cancers.

Furthermore, in order to illustrate the importance of mutations, let's look at the effects of these gene insertion mutations on prognosis. Finally, it is found that the insertion mutation of DIAPH3-AS1, lncRNA, affects the prognosis of the tumor.

The above is the editor for you to share how to use the ICGC database to find a mutation-related topic, if you happen to have similar doubts, you might as well refer to the above analysis to understand. If you want to know more about it, you are welcome to follow the industry information channel.

Welcome to subscribe "Shulou Technology Information " to get latest news, interesting things and hot topics in the IT industry, and controls the hottest and latest Internet news, technology news and IT industry trends.