GEO DataSets

(Submitter supplied) Most of the breast cancer samples used in clinical research contain multiple cell types other than epithelial cells alone. The non-epithelial cell types have have a substantial effect on the gene expression-profile, which is used to define molecular subtypes of the tumours. The purpose of this data set is to retrieve gene-expression profile within tumour epithelial cells. We collected 9 breast cancer epithelial cell lines and 5 tumour sampes from which epithelial cells were sorted and enriched using BerEp4 antibody coated beads. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

14 Samples

Download data: CEL

(Submitter supplied) INTRODUCTION: Basal-phenotype or basal-like breast cancers are characterized by basal epithelium cytokeratin (CK5/14/17) expression, negative estrogen receptor (ER) status and distinct gene expression signature. We studied the clinical and biological features of the basal-phenotype tumors determined by immunohistochemistry (IHC) and cDNA microarrays especially within the ER-negative subgroup. METHODS: IHC was used to evaluate the CK5/14 status of 445 stage II breast cancers. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL3883

100 Samples

Download data: GPR

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL96

508 Samples

Download data: CEL, TXT

(Submitter supplied) Hormones and growth factors accelerate cell proliferation of breast cancer cells, and these molecules are well investigated targets for drug development and application. The mechanisms of cell proliferation of breast cancers lacking estrogen receptor (ER) and HER2 have not been fully understood. The purpose of the present study is to find genes that are differentially expressed in breast cancers and that might significantly contribute to cell proliferation in these cancers. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL8300

40 Samples

Download data: CEL, XLSX

(Submitter supplied) Validation dataset of 298 ER-positive patients treated with tamoxifen for 5 years. All patients in this dataset have ER+ breast cancer and were uniformly treated with tamoxifen for 5 years. The objective of the study was to correlate levels of genomic markers to outcomes (relapse free survival) in this cohort of uniformly treated patients.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL96

298 Samples

Download data: CEL

(Submitter supplied) Comparison of concordance in single and multi-gene genomic indices from data generated by two different laboratories (MD Anderson Cancer Center (MDA) and Jules Bordet Institute (JBI)) and on two different Affymetrix platforms (U113A and U133_Plus2). We used a 2x2 factorial study in which 16 clinical breast cancer samples were profiled by both laboratories on both platforms (64 arrays total).

Organism:

Homo sapiens

Type:

Expression profiling by array

Platforms:

GPL570 GPL96

64 Samples

Download data: CEL

(Submitter supplied) A 36-gene classifier was constructed through expression profiling of 132 tumors from tamoxifen-treated patients using 70-mer oligonucleotide microarrays. The robustness of the signature was demonstrated using expression data from 83 independent tumors. The 36-gene signature was (i) more efficient to predict disease-free survival than the traditional histo-pathological prognostic factors, (ii) as effective as the Nottingham Prognostic Index or the "Adjuvant!" software, and (iii) the only independent prognostic factor. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL5049

155 Samples

Download data: GPR, TXT

(Submitter supplied) Paired FNA and CBX specimens were prospectively collected from 37 breast cancers before any systemic therapy during a biomarker discovery study at The University of Texas M. D. Anderson Cancer Center. We identified 293 probe sets overexpressed in core biopsies; these included five highly coexpressed gene clusters (metagenes) corresponding to immune functions and extracellular matrix components. We compared gene expression profiles of pairs of fine-needle (stroma-poor) and core-needle (stroma-rich) biopsies from 37 cancers to identify stroma-associated genes

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL96

74 Samples

Download data: CEL, TXT

(Submitter supplied) Background: Estrogen receptor positive (ER+) breast cancers (BC) are heterogeneous with regard to their clinical behavior and response to therapies. The ER is currently the best predictor of response to the anti-estrogen agent tamoxifen, yet up to 30-40% of ER+BC will relapse despite tamoxifen treatment. New prognostic biomarkers and further biological understanding of tamoxifen resistance are required. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

77 Samples

Download data: CEL, RDATA, TXT

(Submitter supplied) Purpose: A number of microarray studies have reported distinct molecular profiles of breast cancers (BC): basal-like, ErbB2-like and two to three luminal-like subtypes. These were associated with different clinical outcomes. However, although the basal and the ErbB2 subtypes are repeatedly recognized, identification of estrogen receptor (ER)-positive subtypes has been inconsistent. Refinement of their molecular definition is therefore needed. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platforms:

GPL96 GPL97 GPL570

741 Samples

Download data: CEL, RDATA, TXT

(Submitter supplied) dataset of 60 patients with ER-positive primary breast cancer and treated with tamoxifen monotherapy for 5 years. Data were generated from LCMed cancer cells. Sample_keyword: breast cancer, tamoxifen, recurrence Keywords: other

Organism:

Homo sapiens

Type:

Expression profiling by array

Dataset:

GDS807

Platform:

GPL1223

60 Samples

Download data

Expression profiling of microdissected estrogen positive primary breast cancer tumors from 60 patients. Patients later treated with tamoxifen for 5 years, and tumors grouped according to whether cancer recurred. Results identify markers of disease-free survival that include HOXB13 and IL17BR.

Organism:

Homo sapiens

Type:

Expression profiling by array, log ratio, 2 disease state sets

Platform:

GPL1223

Series:

GSE1378

60 Samples

Download data

(Submitter supplied) Hyperactivation of phosphatidylinositol-3 kinase (PI3K) promotes escape from hormone dependence in estrogen receptor-positive breast cancer. A significant fraction of breast cancers exhibit de novo or acquired resistance to estrogen deprivation. We used gene expression microarrays to identify genes and pathways that are commonly dysregulated in ER+ cell lines with acquired hormone-independent growth. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

24 Samples

Download data: CEL, CHP

(Submitter supplied) To investigate the biological basis between aging and sporadic breast cancer incidence and prognosis, DNA samples from matched ER+ invasive breast cancers diagnosed in either young (<45) or old (>70) women were analyzed with aCGH Keywords: biomarker identification

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platform:

GPL4999

71 Samples

Download data: XLS

(Submitter supplied) To investigate the biological basis between aging and sporadic breast cancer incidence and prognosis, RNA samples from matched ER+ invasive breast cancers diagnosed in either young (≤45) or old (≥70) women were analyzed by expression microarrays Keywords: biomarker identification

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL4685

47 Samples

Download data: CEL

(Submitter supplied) The purpose of this study was to improve prediction of patients at high-risk for metastatic disease utilizing a nested case-control design that uniquely enables enrichment for relevant phenotypes. We identified all women diagnosed with primary breast cancer from January 1, 1997, to December 31, 2005, in the Stockholm health care region. Patients developing distant metastatic disease (cases) were selected and controls (free from distant disease) were randomly matched by adjuvant therapy, age and calendar period at diagnosis. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10379

623 Samples

Download data: CEL

(Submitter supplied) Purpose: To characterize the expression of phosphatases in estrogen receptor negative breast cancer Little is known about the role of phosphatases in the major estrogen receptor negative breast cancer phenotypes (i.e. those overexpressing ERBB2 and the triple negative). We carried out microarray phosphatome profiling in 41 estrogen receptor negative (ER-) breast cancer patients (as determined by immunohistochemistry (IHC)) containing both ERBB2+ and ERBB2- in order to characterize the differences between these groups by Statistical Analysis of Microarrays (SAM). more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL4133

41 Samples

Download data: TXT

(Submitter supplied) Intratumor heterogeneity is one of the hallmarks of cancers, including breast cancers. We performed spatial transcriptomics to profile heterogeneous cell populations within ER+ breast cancers as well as to determine their importance for estrogen-dependent tumor growth. Our analysis has revealed the key functional compartments for developing targeted therapeutic strategies against ER+ breast cancers.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

4 Samples

Download data: CSV, JPG, JSON, MTX, PNG, TSV

(Submitter supplied) Luminal breast cancers are characterized by estrogen-regulated gene profiles. We performed scRNA-seq on a luminal breast cancer PDX named GS1 to profile the gene expression of the cells constituting GS1 tumor and to investigate the effect of estrogen on the individual populations.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

3 Samples

Download data: MTX, TSV

(Submitter supplied) Aminoacyl tRNA synthetases (ARSs) are a class of enzymes with well-conserved housekeeping functions in cellular translation. Recent evidence suggests that ARS genes may participate in a wide array of cellular processes, and may contribute to the pathology of autoimmune disease, cancer, and other diseases. Several studies have suggested a role for the glutamyl prolyl tRNA synthetase (EPRS) in breast cancers, although none has demonstrated any underlying mechanism about how EPRS contributes to carcinogenesis. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

12 Samples

Download data: TXT