Dataset features

Specifications


Application: Gene expression microarray analysis
Number of samples: 58
Release date: Mar 16 2010
Last update date: Mar 21 2012
Access: Public
Diseases: Breast Neoplasms, Neoplasms
Chemicals: Estrogens
Dataset link Identification of subtypes in HER2-positive breast cancer reveals a gene signature prognostic of outcome

Experimental Protocol


Array comparative genomic hybridization (aCGH) identified 58 breast tumors with amplification of HER2 from a larger cohort of approx 500 tumors breast. Global gene expression profiles were obtained using 70-mer oligonucleotide microarrays. Unsupervised hierarchical clustering of the 58 tumors, using Pearson correlation and complete linkage, identified three main clusters. One cluster showed significantly poorer clinical outcome. Significance of microarray (SAM) analysis was performed to identify 158 genes separating the poor outcome cluster compared to the other two clusters. Gene expression centroids, based on the 158 genes, were created for each cluster for validation in independent breast cancer data sets.

Repositories


GEO

GSE18328

ArrayExpress

E-GEOD-18328

BioProject

PRJNA117985

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