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Analysis with FIREHOSE plus TCGA UCSC Xena.

In Brief

  • FIREHOSE Usage.

  • FIREHOSE plus TCGA UCSC Xena.

FIREHOSE Usage

1. Interested Disease from FIREHOSE

  • 1.1 Choose Breast invasive carcinoma.

  • 1.2 Click on Browse of Analyses from Diseases list.

    browsedisease1

2. Get Reports of Analysis

  • Click on BRCA of TCGA data version 2016_01_28 for BRCA to get the reports.

    getreport2

3. Result Analysis

  • In the Results section, choose interested index.

    resultanalysis1

FIREHOSE plus TCGA UCSC Xena

Example 1

  • Click on View Report of Correlations between copy number and mRNAseq expression.

    resultanalysis2

  • Click on Correlation results.

    viewreport1

1. Interested gene, ERBB2

  • Focus on ERBB2 gene, which is very famous gene.

    ERBB2

2. Settings for ERBB2

  • Set up ERBB2 gene on UCSC Xena according to firehose.

    TCGAset

3. Figure 1

  • As show in figure1, r = 0.8617 (p = 0.000), which is almost the same as that of firehose Database.

    figure1

Example 2

  • Click on View Report of Correlation between mRNA expression and DNA methylation.

    resultanalysis3

  • Click on Negative Correlation between Methylation and Gene Expression.

    viewreport2

1. Interested gene, MKRN3

  • Focus on MKRN3 gene, which ranked No.1 in the list.

    MKRN3

2. Settings for MKRN3

  • Set up MKRN3 gene on UCSC Xena according to firehose.

    set2

3. Figure 2

  • As show in figure2, r = -0.8392 (p = 1.538e-232), which is close to that of firehose Database.

    figure2

In Summary

  • Different database resources, but similarly conclusion.

  • Start with preliminary conclusion get from bioinformatics analysis, we can go through to verify by performacing related experiments.

  • Start with verified data from experiments, we can furthermore get supported by bioinformatics analysis.