GEO DataSets

(Submitter supplied) We identified and validated the pivotal role for a metagene containing IFN-induced genes in association to higher metastatic potential as a function of the specific molecular subtype

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6884

123 Samples

Download data: TXT

(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) 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) 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. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL96

218 Samples

Download data: CEL

(Submitter supplied) Estrogen receptor (ER) expression and proliferative activity are established prognostic factors in breast cancer. In a search for additional prognostic motives we analyzed the gene expression patterns of 200 tumors of patients who were not treated by systemic therapy after surgery using a discovery approach. After performing hierarchical cluster analysis, we identified co-regulated genes related to the biological process of proliferation, steroid hormone receptor expression, as well as B cell and T cell infiltration. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL96

200 Samples

Download data: CEL

(Submitter supplied) We treated nine lines of breast cancer cells with conditioned medium derived from NAF and CAF to study the paracrine interaction beetween stroma and tumor. Gene expression profiles for breast cancer cell lines are reported after 72h of treatment with conditioned medium derived from NAF and CAF or with control media.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

87 Samples

Download data: TXT

(Submitter supplied) The FinHER trial is a multicentre phase 3 randomised adjuvant breast cancer trial that enrolled 1010 patients. The women were randomly assigned to receive three cycles of docetaxel or vinorelbine, followed by three cycles of fluorouracil, epirubicin, and cyclophosphamide.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL13667

203 Samples

Download data: CEL

(Submitter supplied) To facilitate a better understanding of the molecular heterogeneity of breast cancer and to uncover gene-survival associations that segregate with distinct molecular subtypes, we recently compiled a meta-analytical database of over 2,000 human breast tumor expression profiles variously annotated for clinical and pathological variables and derived from various institutions worldwide. This database was utilized for the breast tumor study cited below: Nagalla, et. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL96

139 Samples

Download data: CEL, TXT

(Submitter supplied) 15-25% of breast cancers (BC) show ERBB2-amplification and overexpression of the encoded ERBB2 tyrosine kinase receptor. They are associated with a poor prognosis but can benefit from targeted therapy. A better knowledge of these BCs may help understand their behavior and design new therapeutic strategies. In this study, we defined the high resolution genome and gene expression profiles of 54 ERBB2-amplified BCs using 244K oligonucleotide array-comparative genomic hybridization and whole-genome DNA microarrays. more...

Organism:

Homo sapiens

Type:

Expression profiling by array; Genome variation profiling by array

Platforms:

GPL9128 GPL570

109 Samples

Download data: CEL, TXT

(Submitter supplied) Both gene and miRNA expression patterns separately correlate with survival in breast cancer suggesting that the development of models using both miRNAs and gene markers might improve their prediction performance. In this study miRNAs significantly associated with development of distant metastasis were identified and further investigated and validated in the publicly available dataset from the METABRIC. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL8179

123 Samples

Download data: TXT

(Submitter supplied) Current prognostic gene expression profiles for breast cancer mainly reflect proliferation status and are most useful in ER-positive cancers. Triple-negative breast cancers (TNBCs) are clinically heterogeneous, and prognostic markers and biology-based therapies are needed to better treat this disease. We assembled Affymetrix gene expression data for 579 TNBCs and performed unsupervised analysis to define metagenes that distinguish molecular subsets within TNBC. more...

Organism:

Homo sapiens

Type:

Expression profiling by array; Third-party reanalysis

Platform:

GPL96

67 Samples

Download data: CEL, TXT

(Submitter supplied) Mammalian target of rapamycin (mTOR) is a serine/threonine kinase involved in multiple intracellular signaling pathways promoting tumor growth. mTOR is aberrantly activated in a significant portion of breast cancers and is a promising target for treatment. Rapamycin and its analogues are in clinical trials for breast cancer treatment. Patterns of gene expression (metagenes) may also be used to simulate a biologic process of effects of a drug treatment. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

18 Samples

Download data: CEL

(Submitter supplied) Analyses whether, and if so, gene expression can add prognostic information in the subgroups of patients with tumours with low or high proliferative activity. As proliferation measured with MAI and PPH3 has repeatedly been shown to be the best prognosticator in node-negative breast cancer (high sensitivity, little overtreatment).

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6884

94 Samples

Download data: TXT

(Submitter supplied) Total RNA was extracted from FFPE samples of 139 chemotherapy-naïve hormone-receptor-negative breast cancers pooled from three sample sources and assayed for the expression of 21 genes within two previously reported microarray-derived prognostic signatures in 6 RT-PCR multiplexes.

Organism:

Homo sapiens

Type:

Expression profiling by RT-PCR

Platform:

GPL17831

139 Samples

Download data: TXT

(Submitter supplied) Breast cancer molecular subtypes preferentially metastasize to specific organs and the anatomical location of the metastasis is associated with the length of survival post-recurrence. We used microarrays to provide a detailed characterization of breast cancer site-specific metastases with particular focus on identifying genes predictive of breast cancer liver metastatic proprnsity

Organism:

Homo sapiens

Type:

Expression profiling by array

Dataset:

GDS4761

Platform:

GPL10379

91 Samples

Download data: CEL, TXT

Analysis of breast cancer (BC) metastases from different anatomical sites collected prior to treatment. The anatomical location of the metastatic lesion is associated with length of survival post-recurrence. Results provide insight into molecular mechanisms underlying BC site-specific metastases.

Organism:

Homo sapiens

Type:

Expression profiling by array, transformed count, 7 tissue sets

Platform:

GPL10379

Series:

GSE46141

91 Samples

Download data: CEL

(Submitter supplied) This microarray dataset contains 51 triple-negative breast cancers with clinical and recurrence information for at least 3 years of follow-up and 106 luminal breast cancers (reanalyzed data from Series GSE24124, GSE9309, and GSE17040). A novel set of 45-gene signature that was statistically predictive of distant metastasis recurrence for triple-negative breast cancer was identified in this study.

Organism:

Homo sapiens

Type:

Expression profiling by array; Third-party reanalysis

Platform:

GPL7264

51 Samples

Download data: TXT

(Submitter supplied) Interferons are crucial for adaptive immunity and play an important role in the immune landscape of breast cancer. Using microarray-based gene expression analysis, we examined the subtype specific prognostic significance of interferon-γ (IFN-γ) as a single gene as well as an IFN-γ signature covering the signaling pathway in 461 breast cancer patients. Prognostic significance of IFN-γ as well as the IFN-γ signature for metastasis-free survival (MFS) were examined using Kaplan Meier as well as univariate and multivariate Cox regression analyses in the whole cohort and in different molecular subtypes. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL96

461 Samples

Download data: CEL

(Submitter supplied) These data, combined with other cohorts (GSE6532, GSE12093, and qRT-PCR based cohorts), was used to construct the EP algorithm, which predicts the likelihood of developing of a distant recurrence of early stage breast cancer under endocrine treatment. In addition, EPclin, a combination of the EP score, the nodal status and the tumor size, was constructed.

Organism:

Homo sapiens

Type:

Expression profiling by array; Third-party reanalysis

Platform:

GPL96

277 Samples

Download data: CEL, TXT

(Submitter supplied) IL13Rα2 overexpression promotes metastasis of basal-like breast cancers IL13Rα2 depletion in highly metastatic breast cancer cells suppresses lung metastases formation by upregulating TP63 and decreasing their migratory potential

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6244

8 Samples

Download data: CEL, CHP, TXT