Put private data and public Xena Data together via UCSC Xena Hub .

In Brief

  • Load local data.

  • Set up public UCSC Xena data.

  • Local data is from publication Cell Rep. PMID# 29617662.

  • TCGA database is TCGA Prostate Cancer (PRAD).

Load TCGA Database

  • Study: TCGA Prostate Cancer (PRAD).

  • Add 3 columns for ERG: Gene expression, Copy number, Exon expression.

  • Add column for TMPRSS2, Copy number.

  • Add column for chr21, Copy number.

    step 0

Adding In Data From the Literature: ERG-TMPRSS2 fusion

  • Click on View My Data in the top navigation bar and load data.

    step 1

  • Load as Phenotype data.

    step 2

  • Sample ID looks like: TCGA-VP-A87D-01.

    step 3

  • Should suggest Study as TCGA Prostate Cancer (PRAD).

    step 4

  • IMPORT and FINISH.

    step 5

  • Back to Visualization.

    step 6

  • Add Phenotype ERG-TMPRSS2 fusion and generate the final input.

    step 7

In summary, as shown in the last image:

  • About half of the samples have high expression of ERG ( Column B).

  • The high expression of ERG is specifically located in the exons from 3’ end of genes ( Column C).

  • Samples with over-expression of ERG shows a deletion in chromosome 21 ( Column D).

  • Fusion calls agree with expression and Copy number data ( Column EFG).