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This article analyzes how to use cBioportal. The content is detailed and easy to understand. Friends interested in "how to use cBioportal" can read it slowly and deeply along with the ideas of Xiaobian. I hope it can help everyone after reading. Let's learn more about "how to use cBioportal" together with Xiaobian.

cBioportal Tutorial

cBioportal is a website that facilitates the exploration of multidimensional cancer genome data, allowing visual analysis across genes, samples, and data types. Users can visualize patterns of gene changes across multiple samples in a cancer study, compare gene change frequencies across multiple cancer studies, or summarize all relevant genomic changes in an individual tumor sample. The site also supports biological pathway exploration, survival analysis, mutual uniqueness analysis between genetic alterations, selectable data downloads, programming interfaces, and visual summaries that can be used for publication.

Genomic data types integrated into cBioPortal include somatic mutations, DNA copy-number alterations (CNAs), Mrna and microRNA(miRNA) expression, DNA methylation, protein enrichment, and phosphorylated protein enrichment. Currently, the site contains datasets from multiple cancer studies.

The simplified concept of a website is to integrate multiple data types at the gene level and then ask for the presentation of specific biological events in each sample (e.g., gene mutations, gene purity and deletion, gene amplification, up-regulated or down-regulated mRNAs or miRNAs), up-regulated proteins, etc. This allows users to query each gene and each sample for genetic changes and test for recurrence (for certain cancers).

cBioportal is a foreign website, it is best to have vpn when visiting, otherwise it will be slow to open or even open.

Example: Genome and copy number analysis of PTEN gene in liver cancer

Step 1: Select the type of cancer, that is, the subject. The cBioPortal contains at least 32 cancer types and 240 studies, basically covering all common tumors.

Step 2: Select the type of data you want to analyze. The data types here often include the following: Mutations, putative copy-number alterations, mRNA expression z-score. Here we select the default mutations and copy-number alterations.

Step3: Enter the gene PTEN to be analyzed

Analysis after submission

Oncoprint showed that 7% of the samples had gene changes, most of which were PTEN deletions.

2.plot can draw a variety of comparison results, and can change parameters as needed

3.co-expression You can check the correlation between the analyzed gene and other genes

4. View survival curves with comparison/survival plotting

5. Pathway information of the analyzed gene is viewed through the pathway

In addition, a series of analytical results obtained through cBioPortal can be downloaded and saved.

About how to use cBioportal to share here, I hope the above content can make everyone improve. If you want to learn more, please pay more attention to the updates of Xiaobian. Thank you for your attention to the website!

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