GEO DataSets

(Submitter supplied) Purpose HER2 gene amplification or protein overexpression (HER2+) defines a clinically challenging subgroup of breast cancer with variable prognosis and response to therapy. We aimed to investigate the heterogeneous biological appearance and clinical behavior of HER2+ tumors using molecular profiling. Materials and Methods Hierarchical clustering of gene expression data from 58 HER2-amplified tumors of various stage, histological grade and estrogen receptor (ER) status was used to construct a HER2-derived prognostic predictor that was further evaluated in several large independent breast cancer data sets. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL5345

58 Samples

Download data: GPR, TXT

(Submitter supplied) PURPOSE: Current histopathologic systems for classifying breast tumors require evaluation of multiple variables and are often associated with significant interobserver variability. Recent studies suggest that gene expression profiles may represent a promising alternative for clinical cancer classification. Here, we investigated the use of a customized microarray as a potential tool for clinical practice. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL5022

99 Samples

Download data: 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) Predictors built from gene expression data accurately predict ER, PR, and HER2 status, and divide tumor grade into high-grade and low-grade clusters; intermediate-grade tumors are not a unique group. In contrast, gene expression data cannot be used to predict tumor size or lymphatic-vascular invasion. Keywords: disease state analysis

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

129 Samples

Download data: CEL

(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) Medullary breast cancers (MBC) display a basal profile, but a favorable prognosis. We hypothesized that a previously published 368-gene expression signature associated with MBC might serve to define a prognostic classifier in basal cancers. We collected public gene expression and histoclinical data of 2145 invasive early breast adenocarcinomas. We developed a Support Vector Machine (SVM) classifier based on this 368-gene list in a learning set, and tested its predictive performances in an independent validation set. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

266 Samples

Download data: CEL

(Submitter supplied) Obesity is thought to contribute to worse disease outcome in breast cancer as a result of increased levels of adipocyte-secreted endocrine factors, insulin, and insulin-like growth factors (IGFs) that accelerate tumor cell proliferation and impair treatment response. We examined the effects of patient obesity on primary breast tumor gene expression, by profiling transcription of a set of tumors for which the patients’ body mass index (BMI) was ascertained. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL96

103 Samples

Download data: CEL

(Submitter supplied) HER2 gene amplification and protein overexpression (HER2+) define a clinically challenging subgroup of breast cancer with variable prognosis and response to therapy. Although gene expression profiling has identified an ERBB2 molecular subtype of breast cancer, it is clear that HER2+ tumors reside in all molecular subtypes and represent a genomically and biologically heterogeneous group. Genome-wide DNA copy number profiling, using BAC array comparative genomic hybridization (aCGH) were performed on 200 tumors with mixed clinical characteristics and amplification of HER2. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platforms:

GPL9077 GPL7247 GPL4723

200 Samples

Download data: GPR

(Submitter supplied) Gene expression analysis identified a specific signature of differentially expressed genes discriminating good and poor responders in JMML patients. Gene expression signatures were analyzed on two EWOG patient cohorts of pediatric JMML patients. Keywords: Expression data

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

40 Samples

Download data: CEL, CHP

(Submitter supplied) Most solid tumors seem to be organized in a hierarchy in which only a fraction of cells, termed tumor-initiating cells (TICs), is capable of disseminating new tumors after transplantation into recipient mice. However, whether a single TIC can induce a tumor or whether it requires additional TICs or non-TICs for tumor initiation is not known. Here we show that injections of single CD24+:Jag1- cells from Her2/Neu+ mammary tumors into recipient mammary glands induced tumors at a frequency of 1/22. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Dataset:

GDS4099

Platform:

GPL6885

16 Samples

Download data: TXT

(Submitter supplied) The cancer stem cell model maintains that tumors are organized in a hierarchy driven by tumor initiating cells (TICs), and that patient survival inversely correlates with TIC gene expression. Here we generated a prognostic signature for HER2+ breast cancer from TICs purified from MMTV-Her2/Neu mammary tumors. TICs from this model, identified as Lin-:CD24+:JAG1- at a frequency of 2-5% by serial and single cell transplantation assays, showed elevated expression of proliferation genes and low expression of differentiation genes (compared to non-TIC fraction CD24- of the same tumor). more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6246

8 Samples

Download data: CEL

Analysis of primary MMTV-Neu mammary tumors and secondary tumors generated by lin- cell transplantation or by single tumor-initiating cell (TIC) transplantation. Results enable molecular comparisons between the primary and secondary tumors.

Organism:

Mus musculus

Type:

Expression profiling by array, count, 16 specimen, 3 tissue sets

Platform:

GPL6885

Series:

GSE29616

16 Samples

Download data

(Submitter supplied) We sought to determine genes whose expression changed upon treatment with a selective inhibitor of class I PI3 kinase.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

6 Samples

Download data: CEL

(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) In this study, we profiled gene expressions on 20 biopsy tissues of early stage breast carcinoma using Applied Biosystem’s Human Genome Survey Microarrays. Two main previously defined clinically relevant subtypes of breast tumors, Luminal A (longest survival time) and Basal (shortest survival time) were identified. Statistical analysis identified 1210 genes as signature genes characterizing the two subtypes of breast cancer. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platforms:

GPL1843 GPL1426 GPL1708

80 Samples

Download data

(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) [original title] Combined gene expression and genomic profiling define two intrinsic molecular subtypes of urothelial carcinoma and gene signatures for molecular grading and outcome. In the present investigation we sought to refine the classification of urothelial carcinoma by combining information on gene expression, genomic, and gene mutation levels. For these purposes we performed gene expression analysis of 144 carcinomas, and whole genome array-CGH analysis and mutation analyses of FGFR3, PIK3CA, KRAS, HRAS, NRAS, TP53, CDKN2A, and TSC1, in 103 of these cases. more...

Organism:

Homo sapiens

Type:

Expression profiling by array; Genome variation profiling by genome tiling array

Platforms:

GPL4723 GPL5186 GPL3883

285 Samples

Download data: GPR, TXT

(Submitter supplied) When making treatment decisions, oncologists often stratify breast cancers into a low-risk group (ER+, low grade); an intermediate-risk group (ER+, high grade); and a high-risk group that includes Her2+ and triple-negative (ER-/PR-/Her2-) tumors. None of the currently available gene signatures correlates to this clinical classification. We aimed to develop a test that is practical for the oncologists, that offers both molecular characterization of BCs, and improved prediction of prognosis and treatment response. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6104

161 Samples

Download data: TXT