GEO DataSets

(Submitter supplied) Gene expression data from the Nurses' Health Study

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Third-party reanalysis

Platforms:

GPL22920 GPL17585

1577 Samples

Download data: CEL, CSV, TXT

(Submitter supplied) Intrinsic subtyping of breast cancer was performed using an nCounter RUO-PAM50 gene expression assay to determine the ability of instrinsic subtyping to predict what patients may benefit from altered chemotherapy scheduling in the CALGB 9741 clinical trial population.

Organism:

Homo sapiens

Type:

Other

Platform:

GPL21114

1321 Samples

Download data: RCC

(Submitter supplied) A microarray targeting promoters of cancer-related genes was used to evaluate DNA methylation at 935 CpG sites in 517 invasive breast tumors from the Carolina Breast Cancer Study (CBCS), a population-based study of invasive breast cancer. Concensus clustering using methylation (β) values for the 167 most variant CpG loci defined 4 clusters differing most distinctly in hormone receptor (HR) status, intrinsic subtype (luminal versus basal-like) and p53 mutation status. more...

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL9183

526 Samples

Download data: TXT

(Submitter supplied) Investigating the association of alcohol and gene expression of breast tumors and tumor-adjacent tissues.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL22920

1110 Samples

Download data: CEL, XLSX

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

Organism:

Homo sapiens

Type:

Expression profiling by array; Genome variation profiling by SNP array

Platforms:

GPL6801 GPL570

156 Samples

Download data: CEL, CNCHP

(Submitter supplied) We compared expression of 105 breast cancer-related genes between matched primary and metastatic breast cancer

Organism:

Homo sapiens

Type:

Other

Platform:

GPL17071

246 Samples

Download data: TXT

(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 nCounter miRGE™ assay was used to quantify transcript expression with a custom codeset containing probes for 123 endogenous mRNAs and 25 miRNAs to assess the association of genomic markers with long-term breast cancer survival. A total of 1,253 FFPE primary breast cancer samples with high-quality reads were obtained.

Organism:

Homo sapiens

Type:

Other

Platform:

GPL28286

1253 Samples

Download data: RCC, TXT

(Submitter supplied) Background: Obesity is a risk factor for breast cancer in postmenopausal women and is associated with decreased survival and less favorable clinical characteristics such as greater tumor burden, higher grade, and poor prognosis, regardless of menopausal status. Despite the negative impact of obesity on clinical outcome, molecular mechanisms through which excess adiposity influences breast cancer etiology are not well-defined. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL571

424 Samples

Download data: CEL

(Submitter supplied) Human formalin-fixed paraffin-embedded breast tumor tissue (1-4 1.5mm punches) was processed to RNA using High Pure RNA Paraffin Kit (Roche Applied Science, Indianapolis, IN) for quantitative reverse transcription polymerase chain reaction (qRT-PCR).

Organism:

Homo sapiens

Type:

Expression profiling by RT-PCR

Platform:

GPL24747

246 Samples

Download data: TXT

(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) The biological tumor samples (ie, breast tumor specimens) consisted of freshly frozen breast tumors from a population-based cohort of 315 women representing 65% of all breast cancers resected in Uppsala County, Sweden, from January 1, 1987 to December 31, 1989. Estrogen receptor status was determined by biochemical assay as part of the routine clinical procedure. An experienced pathologist determined the Elston-Ellis grades of the tumors, classifying the tumors into low, medium and high-grade tumors. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platforms:

GPL97 GPL96

502 Samples

Download data: CEL

(Submitter supplied) To determine whether breast cancer molecular subtypes and tumor characteristics with demonstrated significance in a primary tumor setting can also confer clinically relevant information in breast cancer metastases. We assessed previously published gene expression modules of seven biological processes and the intrinsic subtypes (PAM50). The translational aspect of the Swedish randomized TEX trial included 112 patients with at least one biopsy from morphologically confirmed loco-regional or distant breast cancer metastasis diagnosed from December 2002 until June 2007. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10379

120 Samples

Download data: CEL

(Submitter supplied) These data can be used for evaluation of the clinical utility of the research-based PAM50 subtype predictor in predicting pathological complete response (pCR) and event-free survival (EFS) in women enrolled in the NeOAdjuvant Herceptin (NOAH) trial. The NeOAdjuvant Herceptin [NOAH] trial demonstrated that trastuzumab significantly improves pCR rates and 3-year event-free survival (EFS) in combination with neoadjuvant chemotherapy compared with neoadjuvant chemotherapy alone in patients with HER2+ breast cancer.

Organism:

Homo sapiens

Type:

Expression profiling by array

Dataset:

GDS5027

Platform:

GPL570

156 Samples

Download data: CEL

Analysis of FFPE core biopsies from pre-treated patients with HER2+ breast cancer (BC) randomized to receive neoadjuvant chemotherapy only or chemotherapy+trastuzumab (herceptin). Results provide insight into the molecular basis of survival outcomes following trastuzumab-based chemotherapy.

Organism:

Homo sapiens

Type:

Expression profiling by array, transformed count, 2 genotype/variation, 2 other, 2 protocol sets

Platform:

GPL570

Series:

GSE50948

156 Samples

Download data: CEL

(Submitter supplied) Activation of inflammatory pathways is one plausible mechanism underlying the association between obesity and increased breast cancer risk. However, macrophage infiltration and local biomarkers of inflammation in breast adipose tissue have seldom been studied in association with obesity. Gene expression profiles of normal breast tissue from reduction mammoplasty patients were evaluated by whole genome microarrays to identify patterns associated with obesity status (normal-weight, body mass index (BMI) <25; overweight, BMI 25-29.9; obese, BMI > or equal to 30). more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL4133

72 Samples

Download data

(Submitter supplied) Cancer progression is mediated by processes that are also important in wound repair. As a result, cancers have been conceptualized as overhealing wounds or "wounds that do not heal," and gene expression signatures reflective of wound repair have shown value as predictors of breast cancer survival. Despite the widespread acknowledgment of commonalities between host responses to wounds and host responses to cancer, the gene expression responses of normal tissue adjacent to cancers have not been well characterized.

Organism:

Homo sapiens

Type:

Expression profiling by array

5 related Platforms

121 Samples

Download data

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

Organism:

Homo sapiens

Type:

Expression profiling by array

Platforms:

GPL13607 GPL4133

433 Samples

Download data: TXT

(Submitter supplied) Activation of the PI3K pathway in estrogen receptor α (ER)-positive (+) breast cancer is associated with reduced ER expression and activity, luminal B subtype, and poor outcome. PTEN is a negative regulator of the PI3K pathway typically lost in ER-negative (-) breast cancer. To clarify the effect of PTEN down-regulation on the response of ER+/HER2- breast cancer to endocrine therapy, we established reduced PTEN cell models using inducible knockdown. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9052

2 Samples

Download data: FPKM_TRACKING