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This article mainly introduces "how to use GDC to view TCGA data online". In daily operation, I believe many people have doubts about how to use GDC to view TCGA data online. Xiaobian consulted all kinds of materials and sorted out simple and easy operation methods. I hope to help you answer the doubts about "how to use GDC to view TCGA data online"! Next, please follow the small series to learn together!

GDC stands for Genomic Data Commons. It is a cancer data sharing system established by the National Cancer Institute of the United States. It integrates information from multiple cancer databases, including TCGA, and provides unified storage, management, display, and sharing of cancer data with cancer genomics researchers worldwide.

https://portal.gdc.cancer.gov/

Data from several large cancer research organizations and projects

Foundation Medicine(FM)

Clinical Proteomic Tumor Analysis Consortium(CPTAC)

THe Cancer Genome Atlas(TCGA)

Therapeutically Applicable Research to Generate Effective Treatments (TARGET)

Human Cancer Model Initiative (HCMI)

The above is only part of the source information, and it is still being updated. In the future, there will be new source data integrated into GDC. Of course, by far the largest data in the database is still from TCGA.

In order to facilitate the management of large amounts of data, a unified data model is established as follows

The highest level is program, which corresponds to different data sources, such as TCGA, TARGET, etc.; the second level is project, which represents a series of patients; the third level is case, which represents all relevant data of the same patient, including SNV, CNV, gene expression profile and other data. It should be noted that case and sample are one-to-many relationships, and a patient can take multiple samples. The last layer is the data associated with each case, i.e. Files. The data types are various, including sequences, gene expression profiles, SNV, CNV, methylation, clinical information and so on.

The above is only a simplified version of the model summarized by the individual, which is easy to understand the information in the database. The actual data type is more, and the model is more complex. The home page of the database provides the following navigation bars

1. project

You can view the data of all projects, or filter through the filter box on the left. The project-related attributes are as follows

primary site indicates the tissue corresponding to the sample, program indicates the data source, disease type indicates the tumor type, data category indicates the data type, such as sequence, SNV, CNV, etc., experimental Strategy indicates the experimental type, such as transcriptome, WGS, methylation chip, etc.

The results in tabular form are shown below

The project id in the first column is composed of program plus tumor corresponding code. The correspondence between tumor name and code is shown as follows

Click project id to view summary information. Take TCGA-BRCA as an example, the following is shown.

2. Exploration

This section supports viewing and filtering data in three ways:

Cases

Genes

Mutations

Cases-related properties are as follows

Genes related attributes are as follows

The attributes associated with Mutations are as follows

Taking Cases as an example, the results are as follows

Click on the case id in the first column to view summary information. In addition, OncoGrid function is also provided to visualize the distribution of SNV and CNV of top50 mutant genes in top200 cases, as shown below.

3. Analysis

This section performs the following two analyses on the filtered data

venn analysis

survival analysis

the results are indicated as follows

4. Repository

This section contains all the available downloaded data, you can view and filter the data from both Files and Cases. The properties related to Files are as follows

Take Files as an example, the results are as follows

By clicking the shopping cart icon, you can add the filtered data set to the shopping cart and download it. For a single data set of interest, you can download it directly by clicking the download button on the web page, but for a large data set, you need to download it through the official client software.

At this point, the study on "how to use GDC to view TCGA data online" is over, hoping to solve everyone's doubts. Theory and practice can better match to help everyone learn, go and try it! If you want to continue learning more relevant knowledge, please continue to pay attention to the website, Xiaobian will continue to strive to bring more practical articles for everyone!

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