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Series GSE4611 Query DataSets for GSE4611
Status Public on Oct 14, 2014
Title Breast Cancer Gene Expression Data from Frankfurt Series
Organism Homo sapiens
Experiment type Expression profiling by array
Summary Pooling of microarray datasets seems to be a reasonable approach to increase sample size when a heterogeneous disease like breast cancer is concerned. Different methods for the adaption of datasets have been used in the literature. We have analyzed influences of these strategies using a pool of 3,030 Affymetrix U133A microarrays from breast cancer samples. We present data on the resulting concordance with biochemical assays of well known parameters and highlight critical pitfalls. We further propose a method for the inference of cutoff values directly from the data without prior knowledge of the true result. The cutoffs derived by this method displayed high specificity and sensitivity. Markers with a bimodal distribution like ER, PgR, and HER2 discriminate different biological subtypes of disease with distinct clinical courses. In contrast, markers displaying a continuous distribution like proliferation markers as Ki67 rather describe the composition of the mixture of cells in the tumor.
Overall design Fresh frozen surgical biopsy samples from consecutive patients were analyzed on Affymetrix HGU133A
Contributor(s) Karn T, Holtrich U, Rody A
Citation(s) 19455418, 17317819, 19272155, 21203899, 18058224, 25274406
Submission date Apr 05, 2006
Last update date Aug 10, 2018
Contact name Thomas Karn
Organization name J.W.Goethe-University
Street address Theodor-Stern-Kai 7
City Frankfurt
ZIP/Postal code 60590
Country Germany
Platforms (1)
GPL96 [HG-U133A] Affymetrix Human Genome U133A Array
Samples (218)
GSM103115 Tumor R-43
GSM103116 Tumor R-44
GSM103117 Tumor R-48
BioProject PRJNA95315

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE4611_RAW.tar 720.9 Mb (http)(custom) TAR (of CEL)
Processed data included within Sample table

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