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This article mainly explains "how to use cBioPortal to view TCGA tumor data", 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 cBioPortal to view TCGA tumor data" bar!

CBioPortal integrates data from TCGA,CCLE and several independent large cancer research projects to build an easy-to-use website that does not require deep computer skills, but can also query, analyze and visualize tumor-related results.

In view of the use of the website, the official released the corresponding article, the link is as follows

Https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4160307/

The URL of the website is as follows

Http://www.cbioportal.org/

A variety of oncology data are stored on this website, which are listed as follows

Somatic mutations

DNA copy-number alterations (CNAs)

MRNA/miRNA expression

DNA methylation

Protein abundance

Phosphoprotein abundance

Regarding the relevant results of each tumor study as a study, it is convenient to explore the data of one or more study. To explore the analysis results of a single study, for example, the process is as follows

You need to go through four steps: the first step is to select the study you are interested in, and the second step is to select the combinatorial data you need to view. In a study, you can include mutations, CNV, expression profiles and other combinatorial data. You can filter some of the data to view. The third step is to select the samples. There is a defined sample list in the database, and the fourth step is to select the genes you need to view. There is already a list of genes corresponding to the pathways studied in the defined tumor in the database. Of course, customization is also supported, as shown below.

After the above four steps, click submit query to view the results. Take the following study as an example

Breast Invasive Carcinoma (TCGA, Cell 2015)

The result page contains the following content

1. OncoPrint

Show the distribution of mutations and CNAs in the sample in the form of a heat map, with one gene for each behavior, and each column represents a sample, as shown below

2. Cancer Type Summary

The composition of mutations and CNAs is shown in the form of a stacked bar chart, as shown below

3. Mutual Exclusivity

Taking the number of samples with mutations in a gene as a set, the corresponding sets of two genes are analyzed to analyze whether the two genes are mutually exclusive or co-occurring in the tumor. the results are as follows

4. Plots

The distribution of samples is visualized through multiple sets of data, and the results are as follows.

5. Mutations

View the details of the mutation sites on each gene, as shown below

6. Co-expression

According to the data of gene expression, the co-expressed genes are analyzed, and the results are as follows.

7. Enrichments

The results of enrichment analysis are shown as follows

8. Survival

The samples are divided into two categories according to whether there are mutations in the query genes, and the differences of survival data between the two types of samples are compared. The results are as follows.

9. CN Segments

Through the IGV Genome browser, view the distribution of CNAs on the chromosome, as shown below

10. Network

Show the interaction network of genes, as shown below

11. Download

Download the data as follows

CBioPortal is very powerful, please refer to the official help documentation for more usage.

Thank you for your reading, the above is the content of "how to use cBioPortal to view TCGA tumor data". After the study of this article, I believe you have a deeper understanding of how to use cBioPortal to view TCGA tumor data, 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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