GEO DataSets

(Submitter supplied) To measures the comparability and concordance of Illumina microarray, a series of 30 samples of Universal Human Reference RNA (UHRR) were set as controls for every single chip of total 30 Human-Ref V2 BeadChips. The average bead number of the 30 arrays was 42.3±8.1 for any bead type over the 22,184 probes. A high average correlation coefficient (r) value was obtained as 0.9908±0077 relative to each other of the expression intensity values from the 30 duplicate UHRR samples.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6104

30 Samples

Download data: 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

(Submitter supplied) In our early study (PMID: 21939527), we have created a ClinicoMolecular Triad Classification (CMTC) to improve prediction and prognostication of breast cancer by using a training cohort contained 161 breast cancer patients (2003 to 2008). Here, a supplemental internal validation cohort contained 340 breast cancer patients was collected (2008 to 2010) for development of the CMTC.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6883

340 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) 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) 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) 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

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(Submitter supplied) To investigate the oxidant sensitivity of E/ER regulated gene expression, E/ER regulated genes are identified using E deprivation or ER-alpha siRNA knockdown; and oxidative stress responsive is determined by 8hr exposure to diamide, hydrogen peroxide and menadione Keywords: biomarker identification

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL3921

12 Samples

Download data: CEL

(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) Signaling pathways that converge on two different transcription factor complexes, NFκB and AP-1, have been identified in estrogen receptor (ER)-positive breast cancers resistant to the antiestrogen, tamoxifen. In this study, biomarkers co-ordinately up-regulated by NFKB and AP-1 with prognositic significance are identified in a largely TAM-treated set of ER+ node negative breast cancers. The prognostic value with respect to age is also investigated. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL4685

54 Samples

Download data: CEL

(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) The behavior of breast cancers and their response to neoadjuvant systemic therapy depend on their phenotype which is to a large extent determined by gene expression programs within the cancer cell. The purpose of the analysis was to compare matched gene expression profiles of pretreatment cancer with post-neoadjuvant systemic therapy, residual cancer.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL96

50 Samples

Download data: CEL

(Submitter supplied) Primary tumors from a series of breast cancer patients evaluated for the presence of tumor cells in bone marrow. Samples were taken at primary surgery, RNA isolated from fresh frozen tumors, amplified and hybridized to 42k cDNA arrays. Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.

Organism:

Homo sapiens

Type:

Expression profiling by array

6 related Platforms

123 Samples

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(Submitter supplied) Today, Radiation therapy (RT) regimens are often used for many types of cancer including breast cancer (BC) disease. BC is an heterogeneous disease, at both clinical and molecular levels, presenting distinct subtypes associated with different clinical outcomes. This variability response may be caused by some factors linked to radiation or dependent to BC specific features such as tumor stage and hormone receptor (HR) status. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL4133

72 Samples

Download data: TXT

(Submitter supplied) Estrogen signals play an important role in the phenotype of estrogen receptor positive breast cancer. However, comprehensive analyses of the effect of estrogen signals on the tumor microenvironment and sur-vival in large cohorts of primary breast cancer patients have been lacking. We aimed to test the hypothesis that estrogen reactivity affects gene expression and immune cell infiltration profiles in the tumor microenvi-ronment and survival.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

112 Samples

Download data: CEL

(Submitter supplied) Identification of predictive markers of response to treatment is a major objective in breast cancer. A major problem in clinical sampling is the variability of RNA templates, requiring accurate management of tumour material and subsequent analyses for future translation in clinical practice. Our aim was to establish the feasibility and reliability of high throughput RNA analysis in a prospective trial. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

226 Samples

Download data: CEL

(Submitter supplied) Paired fine needle aspiration biopsies (FNABs) of breast cancers were taken before (PRE) and after (POST) surgeries from 16 patients and compared the cDNA microarray data to determine the genes that were differentially expressed between the FNABs taken at the two time points. The timing of fine needle aspiration biopsies can be a confounding factor in microarray data analyses in breast cancer. FOS-related genes, which have been implicated in early hypoxia as well as the development of breast cancers, were differentially expressed before and after surgery. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL7025

32 Samples

Download data: GPR

(Submitter supplied) Estrogen receptor (ER) signaling–dependent cancer cell growth is one of the major features of ER-positive breast cancer (BC). Inhibition of ER function is a standard and effective treatment for ER-positive tumors; however, ~20% of patients with ER-positive BC experience early or late recurrence. In this study, we examined intertumor heterogeneity from an epigenetic perspective based on the hypothesis that the intrinsic difference in epigenetic states around ER signaling pathway underlies endocrine therapy resistance. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21697

42 Samples

Download data: BED