Chapter 7 Homepage

7.1 Quick Molecule Exploration

In the top-right of homepage, two modules are provided for quick exploration of cancer molecules.

Quick molecular exploration in the homepage

Figure 7.1: Quick molecular exploration in the homepage

7.1.1 Daily Gene

  1. In this module, a gene will be randomly selected each day and analyzed for which type of TCGA cancer is differentially expressed.
  2. TPM expression data is obtained from TCGA and GTEx samples. For ease of presentation, the samples with minimum expression value of -9.966 are removed.
  3. The wilcoxon test is used, and the cancer with the lowest P value will be displayed via plotly package.
  4. Two external links to GeneCards and PubMed are also provided to search more information about the gene.
  5. Finally, users can sample another gene to perform similar analysis if they want.

7.1.2 Pan-cancer Query

In this module, two functions can be used to explore the pan-cancer features of one multi-omics molecule.

7.1.2.1 Tumor vs. Normal

Observe and compare the molecular values in each TCGA project of normal tissue versus tumor tissue.

Tips: The analysis is based on vis_toil_TvsN() function referring to 5.1

The interface when clicking "Tumor vs. Normal" button

Figure 7.2: The interface when clicking “Tumor vs. Normal” button

7.1.2.2 Generate Report

  1. For general exploration of pan-cancer feature, a well-organized report report can be automatically generated.
  2. As the following figure shows, it firstly run the analyses given the queried molecule, which will take about one minute. Then, you can knit the report in HTML format (figure) or directly download the analyzed results in ZIP format.
The interface when clicking "Generate Report" button and result

Figure 7.3: The interface when clicking “Generate Report” button and result

  1. The report can be generally divided into five parts to describe molecular pan-cancer features, including (1) clinical phenotypes, (2) survival influence, (3) tumor index, (4) immune infiltration, (5) pathway activity.
    Five main parts of molecular report

    Figure 7.4: Five main parts of molecular report

  2. Here is an example report for mRNA TP53.
Head part of demo report

Figure 7.5: Head part of demo report

7.3 TCGA Analysis Guide

  • Based on UCSC Xena datasets, we have designed versatile analyses for TCGA as well as other databases, like PCAWG and CCLE.
  • In the homepage, two series of TCGA analyses, including 12 custom modules (Figure) and 3 personalized pipelines, are displayed as quick interface for users.
12 TCGA analytical modules

Figure 7.7: 12 TCGA analytical modules

3 TCGA analytical pipelines

Figure 7.8: 3 TCGA analytical pipelines