How to analyze TCGA database

This article introduces you how to analyze the TCGA database, the content is very detailed, interested friends can refer to, hope to be helpful to you.

The full name of TCGA is as follows

The Cancer Genome Atlas

It is a cancer research project jointly established by National Cancer Institute (NCI, National Cancer Institute) and National Human Genome Research Institute (NHGRI, National Human Genome Institute). It provides a large, free cancer research reference database by collecting and collating all kinds of cancer-related data.

Currently, there are 33 types of cancer, more than 2 PB data, the data is free and available, greatly helping cancer researchers to improve the prevention, diagnosis and treatment of cancer. The web address of the database is as follows

Https://www.cancer.gov/about-nci/organization/ccg/research/structural-genomics/tcga

Data types include the following

RNA sequencing

MicroRNA sequencing

DNA sequencing

SNP-based platforms

Array-based DNA methylation sequencing

Reverse-phase array (RPPA)

It covers genome, transcriptome, epigenetics, proteome and other genomic data, providing an omni-directional, multi-dimensional data. The official download tool Genomic Data Commons Datga Portal, referred to as GDC, is available at the following URL

Https://portal.gdc.cancer.gov/

There are also many third-party tools, such as

CBioPortal

ForeBrowse

UCSC Xena

The main function of official tools is to view and download data, only a very simple analysis function, while third-party tools focus on TCGA-based data analysis. At present, the commonly used analysis of TCGA data includes the following

Survival analysis

Analysis of the difference between tumor patients and normal subjects

Correlation between histological data and clinical data

Mining based on TCGA and other public databases is a hot topic at present, and TCGA data is often used to map and prove each other with their own actual data in the article. It is imperative to understand and master the use of TCGA data, which will be described in more detail in subsequent articles.

This is the end of the analysis on how to carry out the TCGA database. I hope the above content can be of some help to you and learn more knowledge. If you think the article is good, you can share it for more people to see.