Dataset features

Specifications


Application: Gene expression microarray analysis
Number of samples: 54
Release date: Jan 5 2015
Last update date: Aug 13 2018
Access: Public
Diseases: Neoplasms, Prostatic Neoplasms
Dataset link The hypoxia marker pimonidazole reflects a transcriptional program associated with aggressive prostate cancer.

Experimental Protocol


We combined pimonidazole immunohistochemistry data and expression profiles to identify transcriptional program activated in pimonidazole positive tumors. Whole-genome gene expression profiles were determined in tumor biopsies from an investigation cohort of 46 patients, where 39 patients had received pimonidazole prior to surgery. Gene ontology analysis of 1046 genes upregulated in pimonidazole positive tumors, as defined by a staining fraction above 10%, showed significant enrichment of the biologic processes cell cycle, translation and cellular response to stress. Gene set analysis based on this result identified gene expressions in proliferation, DNA repair and hypoxia response as major parts of the transcriptional program associated with pimonidazole staining. Gene expression data of four prostate cancer cell lines were used to generate hypoxia response gene sets for this analysis. A signature of the 32 most essential genes in the program was constructed and shown to be associated with prostate cancer aggressiveness in two independent validation cohorts.

Repositories


GEO

GSE55935

ArrayExpress

E-GEOD-55935

BioProject

PRJNA241350

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Contact


Heidi Lyng

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