Local UCSC Xena Data Hub

Load the private data to Local Xena Data Hub.

In Brief

The Local Xena Browser is the same as the public browser, which shows same VISUALIZATION and TOOLS no matter where the data is located.

An Application example: Analysis of the total population of monocytes from patients with metastatic breast cancer (MBC), sepsis, or tuberculosis.

Installing a Local Xena Hub

Double click on the download to finish the install.

Dateset Resource

Download related files of GEO accession: GSE65517.

Upload Datasets

• Click on VIEW MY DATA and upload local data: genomicGDS5819_gene-level.tsv and phenotypeGDS5819.tsv.

• Name study: Metastatic Breast Cancer and Sepsis.

  

Add Interested Columns Step by Step

• Back to VISUALIZATION.

• Search for a study, choose Metastatic Breast Cancer and Sepsis.

  

• Add phenotype, choose Disease.

• Add genes: HLA-DRB6, HLA-DRB4, CD86, IL1B, CD83, TNF.

• Dataset: My Computer Hub.

• Choose genomicGDS5819_gene-level.tsv.

• Add column, Add genes: RNASE3, NKG7, OLFM4, CHI3L1, CAMP, LOC653600, PGLYRP1, CTSG, DEFA4, MPO, CEACAM6, BPI, AZU1, CYP4F3, ANXA3, MS4A3, COL17A1, MMP9, ARG1, S100P IL18RAP, CA4, Rgr, TNFAIP6.

  

Adjust Display

• For column C and column D, to click on Display, on the window of Adjust Display Settings, color transformation is be replaced with center by column mean: x - column average.

  

• After adjusting, here is the NEW display.

  

Output

• Analysis figure for the relationship between Disease and column C Genes.

  

• Analysis figure for the relationship between Disease and column D Genes.

  

• Analysis figure for the relationship between Disease and column C Genes, by removing parameter of tuberculosis.

  

• Analysis figure for the relationship between Disease and column D Genes, by removing parameter of tuberculosis.

  

IN SUMMARY, results provide insight into molecular similarities between monocytes from MBC patients and reprogrammed immunosuppressive monocytes from sepsis patients¹.