GEO DataSets

(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 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) Introduction: Overall survival of early-stage breast cancer (BC) patients is similar for those who undergo breast conserving therapy (BCT) and mastectomy, however, 10-15% of women undergoing BCT suffer ipsilateral breast tumor recurrence. The risk of recurrence may vary with age or breast cancer subtype. Understanding the gene expression of the cancer-adjacent tissue and/or stromal response to specific tumor subtypes is important for developing clinical strategies to reduce recurrence risk. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platforms:

GPL16272 GPL4133

71 Samples

Download data

(Submitter supplied) Purpose: Previous studies of breast tissue gene expression have demonstrated that the extratumoral microenvironment has substantial variability across individuals, some of which can be attributed to epidemiologic factors. To evaluate how mammographic density (MD) and breast tissue composition relate to extratumoral microenvironment gene expression, we used data on 121 breast cancer patients from the population-based Polish Women’s Breast Cancer Study.Design: Breast cancer cases were classified based on a previously reported, biologically-defined extratumoral gene expression signature with two subtypes: an Active subtype, which is associated with high expression of genes related to fibrosis and wound response, and an Inactive subtype, which has high expression of cellular adhesion genes. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL4133

120 Samples

Download data

(Submitter supplied) Basal-like breast cancers have several well-characterized distinguishing molecular features, but most of these are features of the cancer cells themselves. The unique stromal-epithelial interactions, and more generally, microenvironmental features of basal-like breast cancers, have not been well characterized. To identify characteristic microenvironment features of basal-like breast cancer, we performed cocultures of several basal-like breast cancer cell lines with fibroblasts (reduction mammoplasty-derived fibroblast line; RMF) and compared these to cocultures of luminal breast cancer cell lines with fibroblasts. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platforms:

GPL4133 GPL8269

99 Samples

Download data

(Submitter supplied) Breast cancer is a profoundly heterogeneous disease with respect to biological and clinical behavior. Gene expression profiling has been used to dissect this complexity and stratify tumors into intrinsic gene expression subtypes associated with distinct biology, patient outcome and different genomic alterations. Additionally, breast tumors occurring in individuals with germline BRCA1 or BRCA2 mutations typically fall into distinct subtypes. more...

Organism:

Homo sapiens

Type:

Expression profiling by array; Genome variation profiling by array

Platforms:

GPL5345 GPL7247 GPL4723

718 Samples

Download data: GPR, TXT

(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) Mechanisms driving tumor progression from less aggressive subtypes to more aggressive states represent key targets for breast cancer therapy. We identified a subset of Luminal A primary breast tumors to give rise to HER2-enriched (HER2E) subtype metastases, but remain clinically HER2 negative (cHER2-). By testing the unique genetic and transcriptomic features of these cases, we developed the hypothesis that fibroblast growth factor receptor 4 (FGFR4) likely participates in this subtype switching. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL20301 GPL16791

166 Samples

Download data: TSV

(Submitter supplied) Mechanisms driving tumor progression from less aggressive subtypes to more aggressive states represent key targets for breast cancer therapy. We identified a subset of Luminal A primary breast tumors to give rise to HER2-enriched (HER2E) subtype metastases, but remain clinically HER2 negative (cHER2-). By testing the unique genetic and transcriptomic features of these cases, we developed the hypothesis that fibroblast growth factor receptor 4 (FGFR4) drives this subtype switching. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

6 Samples

Download data: MTX, TSV

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

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL20311

54 Samples

Download data: TXT

(Submitter supplied) Mechanisms driving tumor progression from less aggressive subtypes to more aggressive states represent key targets for breast cancer therapy. We observed that a subset of Luminal A primary breast tumors give rise to HER2-enriched (HER2E) subtype metastases, but remain clinically HER2 negative (cHER2-). By testing the unique genetic and transcriptomic features of these cases, we developed the hypothesis that FGFR4 drives this subtype switching. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL20311

13 Samples

Download data: TXT

(Submitter supplied) Mechanisms driving tumor progression from less aggressive subtypes to more aggressive states represent key targets for breast cancer therapy. We observed that a subset of Luminal A primary breast tumors give rise to HER2-enriched (HER2E) subtype metastases, but remain clinically HER2 negative (cHER2-). By testing the unique genetic and transcriptomic features of these cases, we developed the hypothesis that FGFR4 drives this subtype switching. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL20311

41 Samples

Download data: TXT

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

Organism:

Homo sapiens

Type:

Expression profiling by array

Platforms:

GPL6884 GPL10558

158 Samples

Download data

(Submitter supplied) Gene expression is widely used for the characterization of breast cancers. Variability due to tissue heterogeneity or measurement error or systematic change due to peri-surgical procedures can affect measurements but is poorly documented. We studied the variability of global gene expression between core-cuts of primary ER+ breast cancers and the impact of delays to tissue stabilization due to sample x-ray and of diagnostic core-cutting. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platforms:

GPL6884 GPL10558

46 Samples

Download data: TXT

(Submitter supplied) Gene expression is widely used for the characterization of breast cancers. Variability due to tissue heterogeneity or measurement error or systematic change due to peri-surgical procedures can affect measurements but is poorly documented. We studied the variability of global gene expression between core-cuts of primary ER+ breast cancers and the impact of delays to tissue stabilization due to sample x-ray and of diagnostic core-cutting. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

112 Samples

Download data: TXT

(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) The cell-type origin has long been suspected to determine molecular features of tumors but has proven difficult to experimentally validate in human breast cancers because of deficiencies in culturing methods that allow propagation of three major cell types of the breast including stem/basal, luminal-progenitor and mature/differentiated cells. We have created immortalized cell lines from core breast biopsies of ancestry-mapped healthy women that are enriched for luminal gene expression including hormonally sensitive ERa-FOXA1-GATA3 transcription factor network. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

59 Samples

Download data: TXT

(Submitter supplied) Breast cancer (BC) is the most commonly diagnosed neoplasm in women worldwide and a well-recognized heterogeneous pathology classified into four molecular subtypes: Luminal A, Luminal B, HER2-enriched and Basal-like, each one with different biological and clinical characteristics. It is well recognize that clinical and molecular heterogeneity of BC is driven in part by mRNA and lncRNAs. We profiled mRNAs and lncRNA in 75 adjuvant tumors using an Affymetrix microarray platform.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL17586

86 Samples

Download data: CEL, CHP

(Submitter supplied) We silenced lncRNA AC009283.1 using shRNAs in cell line SKBR3, carried a ~75% silencing compared to thenegative control (NC). We evaluated the role of lncRNA AC009283.1 on oncogenic phenotypes in the HER2-enriched SKBR3 breast cancer cell line model. The knockdown of lncRNA AC009283.1 was achieved with ~75% of silencing efficiency. A complete transcriptomic analysis after silencing of lncRNA AC009283.1 revealed an impact on the global expression.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL17586

6 Samples

Download data: CEL, CHP

(Submitter supplied) Microarrays have shown that gene expression patterns can be used to molecularly classify breast cancers into distinct and clinically significant groups. In order to translate these profiles into routine diagnostics, we have recapitulated a microarray breast cancer classification using real-time quantitative (q)RT-PCR. We performed statistical analyses on multiple independent microarray datasets to select an “intrinsic” gene set that can classify breast tumors into four different subtypes designated as Luminal, Normal-like, HER2+/ER-, and Basal-like. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platforms:

GPL885 GPL1390 GPL887

126 Samples

Download data